| Method |
Principle |
Discrimination |
Reproducibility |
Data exchange |
Applications |
| Ribotyping |
Hybridization of labelled rDNA with digested genomic DNA |
medium |
good |
possible2 |
Too low discrimination for outbreak analysis (short term epidemiology) |
| RAPID/repPCR
|
PCR with random primers or primers binding to repetitive target sequences |
medium |
insufficient - good1 |
possible2 |
Partly suitable for „in house“ outbreak analyses; provided with commercial kits (DiversiLabTM) |
| AFLP |
Length polymorphisms in genomic PCR products |
good |
good–very good1 |
possible |
Exchanged by MLST due to better data portability and discriminatory power |
| PFGE |
Genome-based macrorestriction analysis |
excellent |
good–very good1 |
possible2 |
Still „Gold-Standard“ for outbreak analyses; not suitable for long term epidemiology / population-based analyses (“over-discrimination“) |
| MLST |
DNA sequence comparisons of housekeeping genes |
good – very good |
excellent |
excellent |
„Gold Standard“ for population-based analyses; comparably expensive and laborious, too less discriminatory for outbreak analyses |
| MLVA |
Fragment length polymorphisms in genomic repeat regions |
good – very good |
very good |
excellent |
Suitable for population-based analyses; too less discriminatory for outbreak analyses |
| vanA cluster typing |
Different schemes exist based on amplification, digestion, sequencing3 |
good – very good |
very good |
good |
Only suitable for specialist analyses and in combination with basic techniques
(PFGE, MLST, MLVA) |
| Plasmid typing |
Analysis of the plasmid content and cmposition3 |
limited |
very good |
possible |
Dependent on the corresponding question; suitable for analysis of “plasmid hospitalism” and for enhancing MLST/MLVA analysis’ results |
| NGS |
Analysis of the genome content |
highest possible |
excellent |
excellent |
its potential for various epidemiological questions has to be analysed in studies in the near future |
Legend: AFLP, Amplified-Fragment Length Polymorphisms; MLST, Multi-locus Sequence Typing; MLVA, Multiple Locus Variable Number of Tandem Repeat Analysis; NGS, Next Generation Sequencing (synonymous for various techniques such as 454, illumina, ion torrent); PFGE, Genomic macrorestriction analysis in Pulsed-field Gel electrophoresis. 1 first specification for Interlab-, second for Intralab reproducability; 