Single- cell genomics reveals population structures from in vitro evolutionary studies of Salmonella

Single- cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for in vitro evolution experiments using FACS isolation of individual bacteria followed by whole- genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of Salmonella in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub- populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high- throughput single- cell sequencing can enhance experimental studies of bacterial evolution.

Automated summary

Single-cell DNA sequencing can reveal hierarchical structures in cell populations and facilitate studies of clonal evolution. This study presents a single bacterial genomic analysis approach for in vitro evolution experiments and applies it to Salmonella's experimental evolution. The results show that the population exposed to antibiotic stress can develop resistance while maintaining diversity. This study demonstrates how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.