Whole Genome Sequencing: Bacterial Typing Revolutionized

Bacterial genotyping, or identifying bacteria at the genetic level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Genotyping also has applications in studying bacterial population dynamics. Over the last two decades, molecular methods have progressively replaced phenotypic assays to type bacterial strains. Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation. We also discussed the application of this technique in a clinical microbiology laboratory, focusing on three essential tasks: (1) identifying the species of an isolate, (2) testing its properties, such as resistance to antibiotics and virulence, and (3) monitoring the emergence and spread of bacterial pathogens. We predict that the application of whole generations sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.