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

Matt Bawn, Johana Hernandez, Eleftheria Trampari, Gaetan Thilliez, Christopher Quince, Mark A. Webber, Robert A. Kingsley, Neil Hall, Iain C. Macaulay

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)
3 Downloads (Pure)


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.
Original languageEnglish
Article number000871
JournalMicrobial Genomics
Issue number9
Publication statusPublished - 20 Sep 2022

Cite this