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

Bawn, Matt, Hernandez, Johana, Trampari, Eleftheria, Thilliez, Gaetan, Quince, Christopher, Webber, Mark A., Kingsley, Robert A. ORCID:, Hall, Neil ORCID: and Macaulay, Iain C. (2022) Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella. Microbial Genomics, 8 (9). ISSN 2057-5858

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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.

Item Type: Article
Additional Information: Funding Information: MB, JH, IM, NH were supported by BBSRC Tools and Resources Development Fund Grant BB/R022526/1. MB, RK, MAW, GT and ET were supported by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10349. NH, MB, IM are also supported by the Core strategic Program of the Earlham Institute BB/CCG1720/1. ICM is supported by a BBSRC New Investigator Grant BB/P022073/1. Next-generation sequencing was delivered via the BBSRC National Capability in Genomics and Single Cell Analysis BB/CCG1720/1 at Earlham Institute.
Uncontrolled Keywords: sdg 3 - good health and well-being ,/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 24 Oct 2022 16:36
Last Modified: 31 Oct 2022 09:30
DOI: 10.1099/mgen.0.000871


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