Deciphering the impact of phages and pathogenicity islands in the emergence of antibiotic resistant bacteria.

Bacteria account for around half of the cells of an average human body and are key determinants of health and disease. How do they evolve? How do multi-resistant and virulent bacterial clones emerge? Bacteria evolve extremely fast in response to environmental challenges, like phage predation or antibiotic therapy, because they mutate and incorporate genes from other bacteria. Horizontal gene transfer (HGT) can, in a single step, transform a benign bacterium into a virulent or drug-resistant pathogen. Bacteriophages, a type of virus that infects bacteria, are important contributors to the diversification of the bacterial genome, either by integrating into the chromosome as prophages or by driving HGT through a process known as genetic transduction. Not only phages but also a new family of pathogenicity islands, the phage-inducible chromosomal islands or PICIs, engage in transduction. This work will investigate the hypothesis that many antibiotic resistance genes, carried in plasmids, are transferred in nature using either phage- or PICI-mediated transduction. We anticipate that using this mechanism, bacteriophages and PICIs must be considered as two of the most important players contributing 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.

Emergence of multi-resistant bacteria is frequently mediated by horizontal transfer of plasmid-encoded antibiotic resistance genes (ARGs), with conjugation classically assumed as the main mechanism driving this transfer. Thus, many plasmids encoding ARGs are either conjugative or can be mobilised by conjugation (mobilisable plasmids). However, hitherto unexplored evidence suggests that other mechanisms of gene transfer must be involved in plasmid mobility. Bacterial genomes frequently contain what are called non-transmissible plasmids, raising the question of how these plasmids spread in nature. Even more surprising is the fact that the size distribution of both mobilisable and non-transmissible plasmids show two peaks: one coinciding with the average size of phages (~40kb) and another with the average size of a new family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Since these plasmids usually encode ARGs, what is the evolutionary force that explains this size distribution? In this project we will analyse the hypothesis that phage- and PICI-mediated generalised transduction are the driving forces responsible for both the transfer of the non-transmissible plasmids in nature and the size distribution observed in the non-conjugative plasmids. This occurs because the transducing particles can mobilise DNA of commensurate size with the phage (packaged in phage capsids) or the PICI (packaged in PICI capsids) genomes. Moreover, we hypothesise here that phages and PICIs impose a trade-off for plasmids between size and mobility, because plasmids that become very large by the acquisition of novel genes may no longer be mobilisable by the same transducing agents. Finally, we will analyse the possibility that transduction can successfully mobilise plasmids between different species and genera, highlighting the critical role for transducing agents in plasmid evolution and antimicrobial resistance transmission in bacterial populations.

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. The discovery that phages and PICIs may promote the transfer of antibiotic resistance genes in nature represents a paradigm shift highlighting the fact that genetic transduction impacts bacterial evolution on a scale that is far greater than we ever imagined. We must decipher the molecular basis and the biological consequences of this extraordinary process of gene transfer. As a result of this programme, new players involved in the emergence of multi-resistant bacterial clones will be discovered. We consider that this paradigm-busting research 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 from the work, both nationally and internationally; 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 animal and human pathogens, and by facilitating the transfer of this knowledge to human and veterinary clinicians.
- Combating infections: Since some antibiotic treatments may increase phage and PICI mediated transfer of virulence and antibiotic resistance genes by generalised transduction, the identification of molecules that could block the packaging and transfer of these genes will be paramount to preventing 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: a BBSRC priority area.