Bacterial single-cell genomics enables phylogenetic analysis of in vitro evolutionary studies [article]

Matt Bawn, Johana Hernandez, Eleftheria Trampari, Gaetan Thilliez, Mark A Webber, Robert A Kingsley, Neil Hall, Iain C Macaulay
2020 bioRxiv   pre-print
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 microbial populations. Here, we present an approach for single bacterial genomic analysis using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to in vitro experimental
more » ... itro experimental evolution of a hypermutator strain of Salmonella in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from the population we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. This population structure could not be resolved from bulk sequence data, and our results show the applicability of high-throughput single-cell sequencing to experimental studies of bacterial evolution.
doi:10.1101/2020.08.25.266213 fatcat:kppoe463lncg3pbh3calutyzye