Newer Methods for Bacterial Strain Typing

Microbial typing is a discipline that has evolved extensively over the past 3 decades. Molecular methods were introduced that essentially replaced phenotyping. Nevertheless, test specificity, data communication, inclusion of population genetics, and automation have been and remain foci of improvement. Present day microbial epidemiologists are inclined to use either DNA repeat- or DNA sequence-based methods; several well-accepted typing schemes have been developed. Repeats were selected as targets because of their elevated mutation rates, which facilitate detailed, multiplexed, real-time microbial fingerprinting. Whether sequencing will ultimately be used for mapping bacterial inter-isolate relatedness remains to be determined, because alternative, technology-driven innovations in typing are frequent. Due to innovative changes in protocol, genomics, proteomics, metabolomics, and spectroscopy are now at a stage to allow their clinical application; these new methods may have advantages that are lacking in current sequencing approaches. This review will outline the current state of typing affairs.