Constant confrontations with microbial threats pose major challenges to human and animal health, agricultural and food production, and public safety. Identifying pathogenic bacteria (species) and tracking strains (by series of well-characterized isolates) to their sources are especially important in outbreak investigations. Compared to the identification of the species, the identification of the source and spread of microbial infections represents a major—and many times futile—challenge. This is due to the multitude of ways microorganisms can occur and spread within healthcare facilities and in the community; how, when, and where they can contaminate the complex nutrition chain, leading to natural and man-made outbreaks.
Typing is the characterization of isolates or strains below species or subspecies level. Typing of bacterial isolates is an essential procedure to identify the microbe causing the illness or to track down an outbreak to the suspected source. In the genomic era, the introduction of molecular methods has largely replaced phenotypic methods and “molecular epidemiology” has emerged as a new discipline. The current molecular typing methods can be classified into three categories: (a) PCR-based methods, (b) DNA fragment analysis-based methods, and (c) DNA sequence-based methods, including the new exciting era of high-throughput genome sequencing.