Biofilm contributions to antimicrobial resistance plasmid transmission

Details

Antimicrobial resistance (AMR) is a major crisis for human medicine. Globally, untreatable bacterial infections are increasing, leaving limited treatment options. Gram-negative Enterobacteriaceae e.g. Klebsiella pneumoniae with carbapenem resistance are classified as critical priorities by the WHO. An important characteristic of bacteria is their ability to share genetic information, including AMR genes, via mobile-genetic elements such as plasmids. Plasmids can share multiple genes producing resistance to clinically important antibiotics such as b-lactams, (including carbapenems), and even drugs-of-last-resort such as colistin. In addition, plasmids can carry genes for increased virulence. Evidence indicates clinically-relevant AMR plasmids persist even in the absence of antibiotics (e.g. Buckner et al, 2018). Pathogens with plasmids carrying AMR genes are responsible for some of the most difficult to treat and often multi-drug resistant infections.

In the real-world, most bacteria live in complex communities called biofilms. These biofilms are difficult to treat, and often form the sources of recalcitrant infections. Growth in a biofilm impacts upon bacterial biology, but also impacts plasmid dynamics and biology (e.g. Element et al 2023). Our aim is to better understand how plasmid transmission occurs within biofilms, and how this biofilm growth influences bacterial and plasmid evolution.

The Buckner lab have developed a flow-cytometry and microscopy-based assay to monitor plasmid transmission and persistence in bacterial populations, using clinically relevant multi-drug resistant bacteria to measure plasmid dynamics (conjugation and persistence) (Buckner et al, mBio, 2020; Alav et al 2026). This system has been optimised for screening for drugs and compounds that inhibit the conjugation and/or persistence of AMR plasmids (termed “anti-plasmid compounds”) (e.g. Alav et al. 2024a, Alav et al. 2024b). In addition, we have collected a library of AMR plasmids, which represent both local and global infections. We have developed long-term evolution experiments enabling comparison between biofilms and planktonic growth of plasmid containing bact.

This project aims to assess how biofilms influence plasmid dynamics and evolution. This project will involve the following specific objectives:

1. Assess contribution of biofilm lifestyles to alterations in plasmid dynamics
2. Determine how growth with anti-plasmid compounds impacts evolution in both planktonic and biofilm cultures
3. Use whole genome sequencing and molecular biology to assess changes in evolutionary trajectories.

The techniques used in this project include: biofilm and planktonic evolutionary experiments, cloning, plasmid conjugation assays (including but not limited to flow cytometry, differential plating), high-throughput drug screening, antimicrobial susceptibility testing, plasmid stability assays, long and short read sequencing, bioinformatics, bacterial phenotypic assays (which may include microscopy, RNA sequencing, biochemical analysis, metabolomics).

Funding Notes

This is a non-funded PhD, therefore the applicant must hold or be applying for independent funding.