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Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori

Nature Ecology & Evolution volume 8, pages 315–324 (2024)Cite this article

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Abstract

Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.

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Fig. 1: Experimental evolution with HGT in antibiotic-free conditions.
Fig. 2: Genomic evolution after 200 generations.
Fig. 3: The evolution of multihit genes and increased transformation rates.
Fig. 4: Selection and rate of HGT determine the probability of reverse evolution.

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Data availability

All data used in this study are available in the supplementary information, and raw sequencing reads have been deposited in GenBank under Bioproject ID: PRJNA907068.

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Acknowledgements

M.J.M. was financially supported by an ARC Discovery Grant (DP220103548) and an NHMRC ideas grant (APP1186140).

Author information

Authors and Affiliations

  1. School of Biological Sciences, Monash University, Clayton, Victoria, Australia

    An N. T. Nguyen, Tim Connallon & Michael J. McDonald

  2. Centre to Impact AMR, Monash University, Clayton, Victoria, Australia

    An N. T. Nguyen & Michael J. McDonald

  3. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia

    An N. T. Nguyen

  4. Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia

    Rebecca Gorrell & Terry Kwok

  5. Department of Microbiology, Monash University, Clayton, Victoria, Australia

    Rebecca Gorrell & Terry Kwok

  6. Biomedical Discovery Institute, Monash University, Clayton, Victoria, Australia

    Terry Kwok

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Contributions

M.J.M. conceived the experiment; A.N.T.N., R.G., T.K. and M.J.M. designed experiments; A.N.T.N. performed experiments; A.N.T.N. carried out sequencing and data analysis; T.C. developed the theory; T.C. and A.N.T.N. performed simulations; A.N.T.N., T.C. and M.J.M. carried out data visualization. All authors wrote the paper.

Corresponding authors

Correspondence to Tim Connallon or Michael J. McDonald.

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Extended data

Extended Data Fig. 1 Replicate transformation efficiency assays.

Transformation efficiency assays for CH426 (purple) and gene deletion mutants for mod3(turquoise) and mod5 (yellow). The assay was repeated three times (N = 3 biologically independent replicates) to account for day and plating effects (A-C). Each coloured dot is an independent plating count for a replicate transformation experiment, empty circles show the mean. Lower bound for the confidence interval not shown where it cannot fit onto the log scale due to being very small, or less than zero.

Extended Data Fig. 2 Accepted parameter values for Approximate Bayesian rejection sampling.

For simulations of a Wright-Fisher model with transformation, selection and drift (grey circles: n = 500 accepted parameter combinations). The black circles and whiskers show the mean and 95% confidence intervals for the two parameters in the accepted parameter sets. The parameter \(\gamma\) denotes the transformation rate relevant to CH428 populations.

Supplementary information

Reporting Summary

Supplementary Data 1

Supplementary Tables 1–8 with raw data and reporting on statistical tests.

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Nguyen, A.N.T., Gorrell, R., Kwok, T. et al. Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori. Nat Ecol Evol 8, 315–324 (2024). https://doi.org/10.1038/s41559-023-02269-5

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