What's Your Subtype? The Epidemiologic Utility of Bacterial Whole-Genome Sequencing

摘要

Determining the source of an infection can be difficult, but it is important for guiding interventions to interrupt outbreaks and prevent infections. Although many pathogens spread by person-to-person transmission, infections can also be acquired from food, animal, insect, or environmental sources. A publication by Eyre et al. in the New England Journal of Medicine sheds light on the source of infection by the bacterium Clostridium difficile by use of a relatively new method of bacterial strain subtyping (1). Bacterial whole genome sequencing (WGS)4 is an emerging, broadly applicable, and powerful technology that has the potential soon to replace multiple functions in research, clinical, and public health microbiology laboratories.Bacterial subtyping determines the similarity between separate isolates of bacteria of the same species. If bacteria have the same subtype, they are more likely to be related to each other than if they have different subtypes. Subtyping is used in epidemiologic investigations to gather information about microbial transmission. For example, if bacteria isolated from 2 patients sharing a hospital room are of the same subtype, the patients might have become infected from a common source or the infection may have been transmitted directly or indirectly from 1 patient to the other, but it is less likely that they acquired the infection from unrelated sources.WGS is 1 of several available methods for bacterial subtyping. WGS generally has greater discriminatory power than other subtyping methods. The discriminatory power of a subtyping method is its ability to differentiate between epidemiologically unrelated strains of bacteria. Many genotypic methods for bacterial subtyping are available with varying discriminatory power (Table 1). Until recently, molecular subtyping methods used only a small fraction of the 3 to 5 million bases in the genomes of most bacterial pathogens. For example, pulsed field gel electrophoresis (PFGE), a restriction fragment length …