Unravelling the impact of lateral transduction in the emergence of antibiotic resistant bacteria.

Horizontal gene transfer can, in a single step, transform a benign bacterium into a virulent or drug-resistant pathogen. Bacteriophages, a type of virus that infects bacteria, drive gene transfer. We have recently identified a new form of gene transfer, lateral transduction, which is the most powerful mode of transduction described to date. Using this mechanism, bacteriophages of Staphylococcus aureus can promote the efficient transfer of hundreds of thousands of bases from the bacterial genome, allowing the bacteria to swap genes and switch from benign to dangerous very quickly. This work will investigate the universality of this mechanism, and identify whether other bacterial pathogens use the same process to evolve in nature. We will also investigate whether this mechanism of gene transfer contributes to the emergence of multi-resistance in clinical strains. This programme will make significant contributions to science, from addressing the molecular basis of fundamental biological processes to understanding the evolution of virulence and the spread of antibiotic resistance in nature.

Bacteriophage-mediated gene transfer is a major evolutionary force occurring by two well-described mechanisms: generalized and specialized transduction. We have recently discovered that Staphylococcus aureus phages engage in lateral transduction, the most powerful mode of transduction described to date. Lateral transduction converts large regions of the bacterial chromosome into "hypermobile platforms" for the high frequency transfer of any genetic element within their boundaries. Bacterial DNA is transferred at astonishingly high frequencies that are at least 1,000 times greater than any known mechanism of transduction. The observed efficiency of chromosomal DNA transfer is unprecedented, representing a paradigm shift in phage biology and in the definition of mobile genetic elements. In this project, analysing important pathogens, we will investigate whether this ground-breaking strategy of gene transfer is widespread in nature. More importantly, we will also analyse here the hypothesis that many mobile genetic elements (i.e. integrons, transposons and integrative and conjugative elements (ICEs)) encoding multiple antibiotic resistance genes, are located in the bacterial chromosome so they can be mobilised both intra- and inter-species by lateral transduction. We anticipate the results of this study will challenge basic and fundamental concepts of phage biology, which will be revisited here. Moreover, the proposed research has the potential to fundamentally re-structure our understanding of the roles of bacteriophages in bacterial evolution, including the development of antimicrobial resistance and virulence in clinical strains.

Bacterial genomes are in constant evolution, with the continual emergence of new virulent clones. However, the mechanistic basis for this process is not well understood. With the rise of superbug strains that are progressively more virulent and antibiotic resistant, the importance of understanding the drivers of bacterial evolution has never been so apparent. Now, the discovery of lateral transduction represents a paradigm shift highlighting the fact that genetic transduction occurs on a scale that is far greater than we ever imagined. We must decipher the molecular basis and the biological consequences of this extraordinary mechanism of gene transfer. As a result of this programme, new players in the field of bacterial virulence and evolution will be discovered. Not only that, this grant will radically change fundamental concepts in the fields of phage biology and genetics: by re-proposing the events that occur after induction of the resident prophages; by involving phages in the emergence of multi-resistant bacterial clones; and by proposing that the bacterial chromosome is more mobile than classical MGEs, just to name a few. We consider that this programme will make significant contributions to science, from addressing the molecular basis of fundamental biological processes to understanding the evolution of virulence and the spread of antibiotic resistance in nature.
Importantly, understanding the biology of this new mechanism of gene transfer, and deciphering how it promotes bacterial evolution, will provide new strategies to prevent the emergence of new virulent and antibiotic resistant clones as well as new strategies to combat bacterial infections.
Because of the multi-faceted, cross-disciplinary and wide-ranging nature of the proposed project, a relatively large number of academic disciplines will benefit, both nationally and internationally, from the work; these include bacteriology, virology, immunology, cell biology and vaccinology. Specifically:
- This project will contribute to the progress of maintaining health and treating diseases by generating an indispensable knowledge base concerning the principles and consequences of a new mechanism of gene transfer in several important human pathogens, and by facilitating the transfer of this knowledge to human and veterinary clinicians.
- Combating infections: Since some antibiotic treatments may increase phage mediated transfer of virulence and antibiotic resistance genes by lateral transduction, the identification of molecules that could block the packaging and transfer of these genes will be prevent the emergence of new virulent and multi-resistant clones.
- Phage therapy: This project highlights that there are unexplored mechanisms of phage-mediated gene transfer that must be characterised in order to safely utilise phages to combat infections. Without this understanding, it is possible that some phage treatments may facilitate the emergence of novel virulent and antibiotic resistant bacterial clones.
- Currently, >75% of bacteriophage and pathogenicity island genes are annotated as hypothetical. This application thus responds to the generally recognised need to translate genome data, and the latest developments in Systems Biology, into sustainable practical applications for medical and veterinary research and treatment.
- This project will unravel a fundamental understanding of the link between phages and disease. This is of general value, because phages play a central role for many pathogenic microorganisms.
In summary, a better understanding of the biology of the different mobile genetic elements, including phages, involved in bacterial virulence is urgently required. The data generated by the experiments proposed here will provide more information into the mechanisms underlying the apparition, spread and emergence of novel bacterial pathogens: an MRC priority area.