The aim of the present study was to evaluate the usefulness of a new typing technique called subtracted restriction fingerprinting (SRF) for bacterial strain and isolate discrimination. The technique was applied to isolates of Salmonella enterica subsp. enterica (S.) serovars Choleraesuis, Typhimurium, Dublin and to two laboratory strains of E. coli. SRF is based on the selective removal of excess fragments from a restriction digest using magnetic particles. Subsequently, the remaining subset of restriction fragments can easily be analyzed with a conventional agarose gel. Larger fragments are preferentially removed by SRF. This results in an even distribution of bands within each electrophoretic lane and significantly improves scoring. The high discriminatory index for (S.) Choleraesuis (D = 0.914) illustrated the suitability of SRF for genome typing.

Reproducible, discriminative, high-throughput methods are required for the identification of bacterial strains and isolates in a clinical environment. A new molecular typing method for bacteria was developed and tested on Salmonella and E. coli species. The technique is called subtracted restriction fingerprinting and is based on double restriction enzyme digestion of genomic DNA followed by end labeling. The detection enzyme produces TTAA overhangs that are filled in with digoxigenated nucleotides for subsequent detection, while the subtraction enzyme produces GCGC overhangs that are filled in with biotinylated nucleotides that permit the removal of this subset of fragments with either streptavidin-coated magnetic particles or AffiniTipTM streptavidin columns. The two restriction enzymes are selected to produce a fragment size profile suitable for a specific analytical system. In this demonstration of the principle of subtracted restriction fingerprinting, analysis of Salmonella enterica subsp. enterica serovar Dublin and E. coli on a 30-cm 1.2% agarose gel revealed up to 50 sharp evenly spaced bands, which were sufficient for the discrimination between various isolates and substrains. The restriction enzyme combinations suitable for the analysis of Salmonella and E. coli are presented. The method requires fewer enzymatic steps than amplified fragment length polymorphism, does not need the specialized DNA preparation essential for pulsed field gel electrophoresis, and has a higher reproducibility than PCR-based methods.

Molecular typing of bacterial pathogens is an important issue in the epidemiological analysis of emerging infections in humans and animals. Numerous methods have been developed for and applied to a wide variety of bacteria of medical, veterinary and zoonotic importance. The present minireview provides a description of a new typing approach designated subtracted restriction fingerprinting (SRF), its use for typing of Salmonella isolates and a comparison with the most widely used typing techniques for these bacteria. SRF is based on double restriction endonuclease digestion of whole cell DNA, followed by a fill-in reaction with specifically tagged nucleotides and subtractive capture of selected restriction fragments. This results in a reduced number of fragments optimal for separation in standard agarose gels.

We have developed a protocol for fast, nonradioactive, mRNA differential display reverse transcription PCR (DDRT-PCR) based on a commercial automated sequencer with RNA isolated from pig granulosa cells. We sought to discover conditions that would minimize the problem of using relatively small primers labeled with large infrared dye molecule, IR41, required for the sequencer. Extended IR41-labeled primers IR41-AAGC-T11-A, IE41-AAGC-T11-C and IR41-AAGC-T11-G gave more consistent differential display patterns than shorter anchored primers (IR41-T11A, IR41-T11C and IR41-T11G) without the additional (AAGC) cloning site. The optimal concentration of the extended labeled (downstream) primers was 20 pmol when 13-mer arbitrary (upstream) primers were used at a concentration of 4 pmol. Background smear and the intensity of amplified bands was significantly improved by changing from conventional Taq DNA polymerase to AmpliTaq Gold polymerase, which permits an improved "hot start" for the reaction. Running time (during which a digitized gel image is recorded) for a 26-cm polyacrylamide gel was 4 h, enabling us to analyze 90 reactions in an 8-h day. This protocol offers a rapid and reliable nonradioactive method for comparing gene expression patterns for various research or diagnostic purposes.

No abstract