Rediscovering plasmid-dependent RNA-bacteriophages: isolation and in vitro evolution of phages to control antibiotic resistance and model viral adaptation to new receptors (RNA-phage)
Main funder
Funder's project number: 347531
Funds granted by main funder (€)
- 480 240,00
Funding program
Project timetable
Project start date: 01/09/2022
Project end date: 31/08/2026
Summary
Plasmid-dependent bacteriophages (phages) are viruses infecting bacteria that bind to plasmid-encoded features on bacterial cells. Some of these phages have been extensively studied (e.g. MS2), but many original isolates collected in 1960s’ to 1980s’ are lost from collections and only few have been discovered ever since. This is despite of their notable potential for applications: plasmid-dependent phages target especially antibiotic resistant bacteria, and their presence selects for the loss of resistance plasmid (i.e. they restore sensitivity to antibiotics). In the time of antibiotic resistance crisis where plasmids are carrying majority of resistance genes and where phages are resurging as an alternative treatment, the rediscovery of plasmid-dependent phages can play a unique role. However, the currently available plasmid-dependent phages cover only a tiny fraction of known resistance plasmids.
Plasmid-dependent (or, in this project pilus-specific) phages are rare (<0.5%) in sewage compared to head-tail phages and hence difficult to find. To tackle this, we collected a library of bacterial hosts that differ in their surface characteristics but can share common pilus-encoding resistance plasmids. This library has been successfully used to filter out majority of head-tail phages and enrich the (still rare) pilus-specific phages. We also aimed to expand the host-range of pilus-specific phage MS2 in a long-term evolution experiment. In this, MS2 is cultivated in the presence of several bacteria with alternative pilus-encoding plasmids. Over the first five months, MS2 has adapted to infect four new plasmids.
The proposed project aims to study the limits for establishing plasmid-dependent phages against any given enterobacterial conjugative resistance plasmid. To meet this goal, we study the adaptation within experimental evolution communities of MS2. We model the evolutionary pace at which MS2 “learns” new receptors and evolutionary pathways for such adaptations. This data is used to determine which pili are within reasonable effort to be targeted via artificial evolution. Further, new MS2-like viruses are isolated and their diversity and characteristics studied to evaluate their availability in environmental reservoirs against a given plasmid type. As a long term goal, the project aims to utilize the collected data to train an artificial intelligence tool which could be employed to design receptor binding proteins against any given pilus protein.
Plasmid-dependent (or, in this project pilus-specific) phages are rare (<0.5%) in sewage compared to head-tail phages and hence difficult to find. To tackle this, we collected a library of bacterial hosts that differ in their surface characteristics but can share common pilus-encoding resistance plasmids. This library has been successfully used to filter out majority of head-tail phages and enrich the (still rare) pilus-specific phages. We also aimed to expand the host-range of pilus-specific phage MS2 in a long-term evolution experiment. In this, MS2 is cultivated in the presence of several bacteria with alternative pilus-encoding plasmids. Over the first five months, MS2 has adapted to infect four new plasmids.
The proposed project aims to study the limits for establishing plasmid-dependent phages against any given enterobacterial conjugative resistance plasmid. To meet this goal, we study the adaptation within experimental evolution communities of MS2. We model the evolutionary pace at which MS2 “learns” new receptors and evolutionary pathways for such adaptations. This data is used to determine which pili are within reasonable effort to be targeted via artificial evolution. Further, new MS2-like viruses are isolated and their diversity and characteristics studied to evaluate their availability in environmental reservoirs against a given plasmid type. As a long term goal, the project aims to utilize the collected data to train an artificial intelligence tool which could be employed to design receptor binding proteins against any given pilus protein.
Principal Investigator
Primary responsible unit
Follow-up groups
Profiling area: Behaviour change, health, and well-being across the lifespan (University of Jyväskylä JYU) BC-Well; School of Wellbeing (University of Jyväskylä JYU) JYU.Well
