In this review, we will focus on recent molecular typing methods that can be applied to different pathogens and assess their values and limitations.
Resistant subgroups within a species of pathogenic organisms often emerge as dominant strains under the selective pressures of antibiotics, vaccinations, and new health care practices. The emergence of resistant organisms has added to the burden and cost of health care-related infections. Pathogens derived from a common ancestry are often difficult to distinguish by conventional methods, and the practice of clinical microbiology and infectious disease epidemiology must adapt to this problem.
Conventional strain typing methods provide a limited means of distinguishing epidemic from endemic or sporadic isolates of pathogens. Nucleic acid-based methods complement conventional and serologic methods of organism isolation and typing. Often, these genomic methods offer more discrimination and details than the phenotype-based conventional methods.
Highly sensitive molecular techniques are capable of detecting single base pair substitutions and resolving the mechanism of underlying complex variation.