applications

BioNumerics software offers an integrated platform for the analysis of PFGE fingerprints. Store all your epidemiological info and gel images in one database. With powerful statistical tools, BioNumerics makes it easy to perform cluster analysis and calculate dendrograms.

Multilocus sequence typing (MLST) is a technique whereby a number of housekeeping genes (loci) are sequenced, usually in part. In a typical MLST approach, recombination is expected to occur with a much higher frequency than point mutations. Therefore, one does not look at the total sequence similarity between strains. Instead, each sequence for a given locus is screened for identity with already known sequences for that locus. If the sequence is different, it is considered to be a new allele and is assigned a unique (arbitrary) allele number.

The TaqMan® SNP genotyping technology utilizes the 5’ nuclease activity of Taq polymerase to generate a fluorescent signal during PCR. For each SNP, the assay uses two TaqMan® probes that differ in sequence only at the SNP site, with one probe complementary to the wild-type allele and the other to the variant allele. The technique utilizes the FRET technology whereby a 5’ reporter dye and a 3’ quencher dye are covalently linked to the wild-type and variant allele probes.

Bacterial community fingerprinting refers to a number of cultivation-independent methods that are used to measure biodiversity in environmental samples or to profile microbial community structures, e.g. in response to experimental conditions.

The DiversiLab™ System (bioMérieux) is an automated DNA fingerprinting system based on the rep-PCR electrophoresis technique.

Antimicrobial susceptibility is expressed either as a Minimum Inhibitory Concentration (MIC), determined via serial dilution or Etest, or as an inhibition zone diameter when determined via the disk diffusion method. Using the Antibiotics susceptibility plugin in BioNumerics, cut-off values can be set and antibiotic resistance data automatically converted to SIR categories (Susceptible, Intermediate, Resistant), which can then be used for calculating dendrograms and to perform statistical analyses on.

The spa typing technique uses the sequence of a polymorphic VNTR in the 3' coding region of the S. aureus-specific staphylococcal protein A (spa). Each new base composition of the polymorphic repeat found in a strain is assigned a unique repeat code. The repeat succession for a given strain determines its spa type.

Variable-Number Tandem Repeats (VNTR's) are well known for their high mutation rate and are therefore widely used for subtyping. Some VNTR's, however, exhibit polymorphism in their individual repeat sequences. By sequencing the polymorphic repeat region, each new repeat variant determined can be assigned a unique repeat code. The repeat succession for a given strain in turn, determines that strain's VNTR type.