DNA-based identification systems for pathogenic bacterial species and strains

DNA-based identification systems for bacteria are often referred to as genotyping methods, making st clear distinction between this approach and the more classical phenotyping methods. While many phenotyping methods are still in widespread use in studies on food hygiene and other microbiology related topics, it seems inevitable that they will soon be replaced by various DNA-based systems. The last decade has seen an exponential increase in the number of published genotyping methods, and it may seem to the practising microbiologist like an insurmountable task to gain an understanding of all these systems. Luckily, only a handful of the methods to date have gained widespread acceptance in applied bacteriology; these methods and their respective underlying theoretical basis are presented below.