Exploring antimicrobial resistance in the human gut microbiome

Secondary Supervisor(s): Dr Richard Horniblow

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Microbiology)

Project Outline

Antimicrobial resistance (AMR) is a serious global health problem. AMR genes can be easily shared between bacteria on transmissible elements such as plasmids. AMR plasmids carry some of the most serious resistance genes, causing difficult to treat infections. Particularly problematic are carbapenem resistant Klebsiella pneumoniae and extended-spectrum beta-lactam resistant Escherichia coli. Pathogens with plasmids carrying AMR genes are responsible for some of the most difficult to treat and often multi-drug resistant infections.

A key hotspot for the transmission of AMR between bacteria is the gastrointestinal (GI) microbiome. For example, AMR genes can be acquired after travel to countries with high AMR levels, or after medical care. This makes the microbiome an important reservoir of AMR, and a key environment where AMR transmission is likely to occur. This project will make use of a state-of-the-art multi-vessel bioreactor model of the colonic microbiome (MIMic; Horniblow, 2nd supervisor), to explore how small molecules produced by the microbiome influence AMR plasmid behaviour.

We propose using a combination of classical microbiology and fluorescent based techniques to uncover some of the mechanisms underlying microbiome manipulation of AMR plasmid dynamics.

Objectives

1) Quantify how supplements and drug treatment influences AMR plasmid dynamicswithin the bioreactor colonic microbiome. This will be done by inoculating MIMic (contains human GI microbiome) with clinical plasmids conferring resistance to carbapenems and/or cephalosporins in K. pneumoniae and E. coli, with or without treatment including dietary supplements and drugs such as antibiotics. The plasmids used here are studied in the Buckner lab. Samples will be taken regularly and:

(a) used to calculate AMR plasmid abundance.

(b) isolate plasmid-bearing cells that have received the plasmid (transconjugants). We will quantify and isolate transconjugants using selective plating, flow cytometry and FACS.

(c) used to determine how supplementation/drug treatment impacts the composition of the microbiome

(d) stored for future genetic, microbiological and/or metabolomic analysis.

This will answer questions about how changes in the microbiome that result from supplementation or treatment alter the length of carriage of AMR plasmids, and rates of plasmid transfer.

2) Determine impact of compounds with anti-plasmid activity on AMR plasmid dynamics in the microbiome. Buckner’s lab have been exploring putative anti-plasmid compounds, which inhibit conjugation (e.g. Buckner et al 2020, Alav et al 2024 a & b). Here we will test whether compounds are effective in preventing AMR transmission within the microbiome. This will answer questions about which compounds are most likely to be effective treatments to reduce AMR prevalence within bacterial populations.

Together this project will help to disentangle how AMR transmission in the microbiome occurs and contribute to our efforts to minimise the impacts of AMR.