Characterisation based on the DNA/RNA sequence of molecular markers (housekeeping, rRNA, virulence, drug-resistance genes, etc.). Analysis of several markers (Multi-Locus Sequence Analysis/Typing, MLSA/MLST) allowing strain typing
| Technique or Methodology | Description |
|---|
| Gene sequencing | DNA amplification by PCR of the gene(s) of interest, followed by sequencing of the amplified fragments |
Strain typing based on differences in the DNA sequence of the isolates or environmental samples. Used, for example, for strain typing/differentiation, for phylogenetic analysis or to study the microbial diversity of environmental samples. The service includes consultancy to define the most suitable method considering the type of sample or the taxonomic group of the strain of interest
| Technique or Methodology | Description |
|---|
| Random Amplification of Polymorphic DNA (RAPD) | DNA amplification by PCR with a single oligonucleotide that hybridizes randomly to the DNA under study, which generates a unique fingerprint of each isolate |
| Denaturing Gel Gradient Electrophoresis (DGGE) | DNA amplification by PCR of a fragment from a region of interest (fixed size), followed by separation of the fragments in a gel electrophoresis with an increasing denaturing gradient. This method can detect single base changes/mutations in environmental samples |
| Temporal temperature gradient gel electrophoresis (TTGE) | DNA amplification by PCR of a conserved molecular marker followed by separation of the fragments in a denaturing acrylamide gel electrophoresis under a gradient of temperature. Used to study the microbial diversity of an environmental sample |
| Amplified Fragment Length Polymorphism (AFLP) | Digestion of the genomic DNA with specific restriction enzymes followed by amplification by PCR, which generates a unique fingerprint of each isolate |
| Microsatellites or Simple Sequences Repeats (SSR) | DNA amplification by PCR of microsatellite regions, which generates a unique fingerprint of each isolate |
| Repetitive element palindromic PCR (rep-PCR) | DNA amplification by PCR of extragenic repetitive palindromic elements, which generates a unique fingerprint of each isolate |
| Inter-LTR | DNA amplification by PCR of sequences separating Long Terminal Repeats retrotransposons, which generates a unique fingerprint of each isolate |
| Genomic restriction fragment length polymorphisms (RFLP) | Digestion of the genomic DNA with specific restriction enzymes, which generates a unique fingerprint of each isolate |
| Mitochondrial restriction fragment length polymorphisms(mt-RFLP) | Digestion of the mitochondrial DNA with specific restriction enzymes, which generates a unique fingerprint of each isolate |
| Amplified Ribosomal DNA Restriction Analysis (ARDRA) | DNA amplification by PCR of the 16S rDNA gene, followed by digestion with specific restriction enzymes, which generates a unique fingerprint of each isolate. Can be used to make phylogenetic studies of environmental samples by cloning the 16S rDNA genes of the sample |
| Ribotyping | Digestion of the genomic DNA with specific restriction enzymes and hybridization with a ribosomal (rRNA) probe, to analyse the number and sequence diversity of the rRNA operons |
High-throughput dereplication screening using MALDI-TOF MS to group isolates that represent the same taxon. Used to reduce a large number of isolates to a smaller, non-redundant set for further characterization
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Separation of intact chromosomal DNAs by pulsed field gel electrophoresis (PFGE) to type at inter- and intra-specific level
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Estimation of the number of copies of single chromosomes using flow cytometry and specific florescent dyes targeting DNA
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Characterisation of a strain based on presence, size and copy number of its plasmids. Used to type bacterial isolates
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