Loop-mediated amplification as promising on-site detection approach for Legionella pneumophila and Legionella spp.

Recently Legionella pneumophila is the main causative waterborne organism of severe respiratory infections. Additionally, other Legionella species are documented as human pathogens. In our work, we describe a rapid detection method which combines two advantages for sensitive and specific detection of the genus Legionella: the fast isothermal amplification method "Loop-mediated isothermal AMPlification" (LAMP), and a colorimetric detection method using the metal indicator hydroxynaphtol blue (HBN) which allows to determine an optical signal with a simple readout (with the naked eye). Moreover, we present two approaches for minimizing the assay volume using a stationary microchip LAMP and droplet digital-based LAMP (ddLAMP) as promising highly sensitive setups.

Agrimonia procera exerts antimicrobial effects, modulates the expression of defensins and cytokines in colonocytes and increases the immune response in lipopolysaccharide-challenged piglets.

BACKGROUND: Because antibiotic use in livestock is assumed to contribute to the emerging public health crisis of antibiotic resistance, alternatives are required. Phytogenic additives are extensively studied due to their antibiotic properties. Components of Agrimonia species have been reported as candidate antimicrobials that possess antioxidative and anti-inflammatory properties. We studied the impact of Agrimonia procera (AP) on the growth of selected strains of gut bacteria, the effect of AP on the mRNA abundance of genes involved in inflammation and bacterial defense in a colon carcinoma cell line, the effect of AP in piglets challenged with lipopolysaccharides, and the effect of AP on the growth performance of healthy piglets. RESULTS: The in vitro growth rate of different bacteria strains was negatively affected by AP, especially in Pediococcus pentosaceus and all tested E. coli strains. Stimulation of Caco-2 cells with TNFα resulted in elevated mRNA expression of CXCL1, IL-8 and GPX2. After pretreatment of cells with AP, stimulation of Caco-2 cells with TNFα still resulted in elevated mRNA expression of CXCL1 and IL-8 at all measured points in time. However, mRNA expression in AP-pretreated cells was lower after 6 h and 24 h. In addition, expression of DEFB1 and GPX2 was significantly elevated after TNFα stimulation. In vivo, application of lipopolysaccharides induced significantly increased animal body temperatures. Piglets pretreated with AP prior to lipopolysaccharide application showed a faster and larger increase in body temperature than controls. In addition, piglets pretreated with AP appeared to release more TNFα than controls. In healthy piglets, AP treatment had no impact on growth performance parameters. Fecal dry matter and total plasma antioxidant capacity tended to be higher in piglets treated with AP than in control piglets (P = 0.055 and P = 0.087, respectively). CONCLUSIONS: AP has antimicrobial effects in vitro and stimulated the expression of proinflammatory cytokines in Caco-2 cells. The additive had no effect on growth in healthy piglets but increased the immune response in LPS-treated animals. In addition, AP appeared to have antioxidative effects in vivo. Therefore, AP merits testing as a future alternative to antibiotics in animal husbandry.

Quality control of inclusion bodies in Escherichia coli.

BACKGROUND: Bacterial inclusion bodies (IBs) are key intermediates for protein production. Their quality affects the refolding yield and further purification. Recent functional and structural studies have revealed that IBs are not dead-end aggregates but undergo dynamic changes, including aggregation, refunctionalization of the protein and proteolysis. Both, aggregation of the folding intermediates and turnover of IBs are influenced by the cellular situation and a number of well-studied chaperones and proteases are included. IBs mostly contain only minor impurities and are relatively homogenous. RESULTS: IBs of alpha-glucosidase of Saccharomyces cerevisiae after overproduction in Escherichia coli contain a large amount of (at least 12 different) major product fragments, as revealed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE). Matrix-Assisted-Laser-Desorption/Ionization-Time-Of-Flight Mass-Spectrometry (MALDI-ToF MS) identification showed that these fragments contain either the N- or the C-terminus of the protein, therefore indicate that these IBs are at least partially created by proteolytic action. Expression of alpha-glucosidase in single knockout mutants for the major proteases ClpP, Lon, OmpT and FtsH which are known to be involved in the heat shock like response to production of recombinant proteins or to the degradation of IB proteins, clpP, lon, ompT, and ftsH did not influence the fragment pattern or the composition of the IBs. The quality of the IBs was also not influenced by the sampling time, cultivation medium (complex and mineral salt medium), production strategy (shake flask, fed-batch fermentation process), production strength (T5-lac or T7 promoter), strain background (K-12 or BL21), or addition of different protease inhibitors during IB preparation. CONCLUSIONS: alpha-glucosidase is fragmented before aggregation, but neither by proteolytic action on the IBs by the common major proteases, nor during downstream IB preparation. Different fragments co-aggregate in the process of IB formation together with the full-length product. Other intracellular proteases than ClpP or Lon must be responsible for fragmentation. Reaggregation of protease-stable alpha-glucosidase fragments during in situ disintegration of the existing IBs does not seem to occur.

RNA-based sandwich hybridisation method for detection of lactic acid bacteria in brewery samples.

Recently we showed the applicability and sensitivity of the RNA-based sandwich hybridisation assay (SHA) for detection of gram-negative cells in environmental samples [Leskelä, T., Tilsala-Timisjärvi, A., Kusnetsov, J., Neubauer, P., Breitenstein, A., 2005. Sensitive genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay. J. Microbiol. Met. 62, 167-179.]. In this study the aim was to test and optimise this method for the detection of gram-positive cells from brewery yeast slurries that contain up to 10(9) yeast cells/ml. Eleven new oligonucleotide probes were designed for group-specific detection of different beer-spoiling lactic acid bacteria of the genera Lactobacillus and Pediococcus. Functionality of the designed probes was shown by testing individual and paired probes using in vitro transcribed 16S rRNA and crude cell extracts as samples. Various simple and fast cell disruption methods were evaluated for the efficient disruption of lactobacilli and pediococci. The applicability of the designed oligonucleotide probes and the SHA for detection of brewery contaminants was demonstrated using both artificial and actual yeast slurry samples from brewery fermentation tanks with either fluorimetric readout or an electric biochip analyser.

16S rRNA targeted sandwich hybridization method for direct quantification of mycobacteria in soils.

Boreal soils have been suspected reservoirs of infectious environmental mycobacteria. Detection of these bacteria in the environment is hampered by their slow growth. We applied a quantitative sandwich hybridization approach for direct detection of mycobacterial 16S rRNA in soil without a nucleic acid amplification step. The numbers of mycobacterial 16S rRNA molecules found in the soil indicated the presence of up to 10(7) to 10(8) mycobacterial cells per gram of soil. These numbers exceed by factor of 10 to 100 x the previous estimates of mycobacteria in soil based on culture methods. When real-time PCR with mycobacteria targeting primers was used to estimate the number of 16S rDNA copies in soil, one copy of 16S rDNA was detected per 10(4) copies of 16S rRNA. This is close to the number of 16S rRNA molecules detected per cell by the same method in laboratory pure cultures of M. chlorophenolicum. Therefore a major part of the mycobacterial DNA in the studied soils may thus have represented metabolically active cells. The 16S rRNA sandwich hybridization method described in this paper offers a culture independent solution for tracking environmental reservoirs of viable and potentially infectious mycobacteria.

Sensitive genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay.

The aim of this study was to develop a sensitive, cultivation-independent analytical method for Legionella in man-made water systems which can be performed within one day in crude sample extracts. The new assay for the genus Legionella is a paramagnetic bead based fluorescence sandwich hybridization assay (SHA) for the 16S rRNA based on two oligonucleotide probes which makes the method highly specific. An advantage over RT-PCR is the exclusive detection of viable cells and, due to the high number of 16S RNA molecules, the possibility to apply the method directly in crude cell extracts without prior purification of the nucleic acids. A high sensitivity was obtained by modifying the probe chemistry and hybridization conditions. The most sensitive assay uses a 3'-end biotin-labelled capture probe and a 3'-end DIG tailed detection probe and has a detection limit of 20 amol target molecules corresponding to 1.2x10(7) molecules of 16S rRNA and approximately 1800 Legionella cells. Using this assay type the number of Legionella cells was determined in Legionella contaminated water samples. The results show that the developed SHA can be applied for estimation of the approximate number of Legionella cells based on the number of 16S rRNA molecules in a water sample.

Sandwich hybridisation assay for quantitative detection of yeast RNAs in crude cell lysates.

BACKGROUND: A rapid microtiter plate based sandwich hybridization assay was developed for detection and quantification of single RNA species using magnetic beads. Following solution hybridization target RNA molecules were collected by biotin-streptavidin affinity binding and detected by fluorescence signal generated by alkaline phosphatase. The 18S rRNA and SUC2 mRNA of Saccharomyces cerevisiae were used as model RNA target molecules. RESULTS: The sensitivity of the assay was approximately 1.2 x 109 (2 fmol) molecules of target RNA. The developed method was feasible with crude cell lysates of S. cerevisiae carlsbergensis and was evaluated by measuring the levels of 18S rRNA during cell growth and SUC2 mRNA under repressive and inductive conditions. The 18S rRNA expression level followed the changes in the specific growth rate. SUC2 mRNA levels were in good correlation with the measured invertase enzyme activities. CONCLUSIONS: The here presented sandwich hybridisation method was succefully applied for monitoring the amounts of ribosomal RNA and mRNA with high expression level in shake flask cultivation conditions. Sandwich hybridisation method offers a fast and convenient tool for following single key RNA species of interest in the production conditions.

Reclassification of Clostridium hydroxybenzoicum as Sedimentibacter hydroxybenzoicus gen. nov., comb. nov., and description of Sedimentibacter saalensis sp. nov..

Strain ZF2T, isolated from freshwater sediment, is a motile, rod-shaped, gram-positive, endospore-forming, amino acid- and pyruvate-utilizing, anaerobic bacterium. It requires yeast extract for growth. Carbohydrates are not utilized. The optimal temperature and pH for growth are 37 degrees C and 6.8-7.3, respectively. The G+C content of the DNA is 34.0 mol %. A 16S rDNA sequence analysis of strain ZF2T revealed that the highest similarity (94.4%) was shared with Clostridium hydroxybenzoicum JW/Z-1T. Strain ZF2T, however, was not able to carboxylate phenol or to decarboxylate 4-hydroxybenzoate, which are characteristic properties of strain JW/Z-1T. The degree of 16S rDNA relatedness, together with the physiological and chemotaxonomic properties, suggest that strain ZF2T represents a novel species that is clearly distinct from Clostridium hydroxybenzoicum JW/Z-1T. In a phylogenetic dendrogram, both strains form a separate cluster that is peripherally associated with the Peptostreptococcus group (cluster XIII) of the clostridia and the lineage of Helcococcus kunzii. Strains ZF2T and JW/Z-1T show a somewhat deeper branching from the cluster XII clostridia Clostridium purinolyticum and Clostridium acidiurici. The latter strains possessed the closest 16S rDNA similarity (between 88.4 and 90.7%), but were clearly separated by phenotypic markers. Therefore, a new genus, Sedimentibacter gen. nov., is described, comprising Sedimentibacter hydroxybenzoicus gen. nov., comb. nov., as the type species of the genus, with JW/Z-1T (= ATCC 51151T = DSM 7310T) as the type strain, and the novel species Sedimentibacter saalensis sp. nov., with strain ZF2T (= DSM 13558T = ATCC BAA-283T) as the type strain.