The main purpose of microbial typing is to evaluate the relationships between microbial isolates. Microbial typing can use for identifying the source of infection by detecting a clonal link between the strains. Moreover, it can analyze outbreaks, antimicrobial-resistant strains, and evaluate the effectiveness of control measures so, the efficiency of monitoring systems would increase. HAIs can affect hospitalized patients in all age ranges with any clinical situation, and lead to death. Molecular epidemiology is useful to determine genetic relatedness between isolated pathogens from patients, and design proper prevention plans to prevent infection through the hospital and community. Nowadays, typing methods for a wide range of bacterial strains are known as essential epidemiological tools to prevent and control infections in hospitals and communities. Although basic typing methods were more focused on phenotypic techniques like antibiogram and serotyping, new methods are based on molecular techniques including PCR-based methods and sequencing-based methods. Due to the high frequency of methods, choosing the right one for research applications seems difficult and requires basic knowledge about all of them. In this review, we aim to introduce the most useful and practical molecular typing techniques. Also, their utilization, advantages, and disadvantages were compared.
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