Population sequencing can now efficiently reveal phylogenetic diversity in bacterial pathogens

What is it about?

Evolutionary relationships among genomic variants in a single bacterial population can reveal clues about, adaptation, persistence, and transmission dynamics. However, the cost and effort of sequencing a representative number of colonies to characterize a population has limited research to thorough sampling of select cases or broader, but cursory examinations across multiple cases. Sequencing directly from a mixed population shows variants, but they cannot be linked to reveal evolutionary patterns. Here, we introduce a hybrid isolate and population sequencing approach to efficiently characterize diversity and leverage the power of phylogenetic approaches for high throughput studies of carriage and transmission. We demonstrate the utility of this approach with examples of pathogen compartmentalization, spread between body sites, and transmission between individuals.

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Photo by National Institute of Allergy and Infectious Diseases on Unsplash

Photo by National Institute of Allergy and Infectious Diseases on Unsplash

Why is it important?

Current sequencing methods provide the ability to deeply sample a population, but the theory and method for deriving phylogenetic information from such mixed samples has not previously been developed. Our method opens the door for high throughput studies as it only requires a single isolate and a population sample (from broth or a plate sweep) to be sequenced. This method provides unmatched genotypic resolution and even, for the first time, allows for determination of spread between body sites. Not only does this allow us to revisit typical carriage-related questions (i.e., strain persistence/turnover, reservoir sites, and transmission direction) in a more efficient and thorough manner, but it also allows us to address questions that have not previously been tackled (i.e., asymptomatic spread between body sites).

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