Saving our last-line antimicrobials

Abstract

During the past decade, an increasing number of bacterial pathogens have developed resistance mechanisms against beta-lactam (BL) antibiotics, most commonly by acquisition of genes that encode for enzymes de-activating the BLs, so-called beta-lactamases (BLAs). One tactic to counter this is to combine the BLs with inhibitors; small molecules that bind to the bacterial enzymes, rendering the bacteria de facto sensitive to the antimicrobial. This has been a fruitful area of drug discovery, with 40% of the 32 antibiotics active against WHO priority pathogens in the pre-clinical pipeline in this category.

However, an increasing number of bacteria have recently become identified that are able to counter the BL + inhibitor combinations by increasing the expression of their BLAs which can occur via a combination of strong promoters causing increased gene expression, and/or increases of the gene copy number either via increased numbers of a plasmid or by gene duplication via mobile elements.

Two major new BL + inhibitor combinations of last resort are ceftazidime/avibactam and meropenem/vaborbactam, which are now used for carbapenem resistant infections in the UK and globally.   However, it is unclear whether resistance to these last-line antimicrobials will also occur via similar mechanisms.

You will use a combination of laboratory experiments and bioinformatics to disentangle the different resistance strategies used by clinical isolates of the Gram-negative pathogens Escherichia coli and Klebsiella pneumoniae, analyse the genomic context and population genomics to understand the spread and transmission of these mechanisms, and targeted transcriptomics (including single-cell) to investigate the impact of these mechanisms on the whole regulatory network and the bacteria’s fitness. A translational question specifically addressed will be if an increase of the inhibitor concentration, or the use of other antibiotics in combination can counter some or all of these resistance mechanisms. This would be a comparatively straightforward change in treatment regimen that could potentially rescue the use of the relevant BLs from the respective resistance mechanisms.

There will be opportunity to carry out work with clinical and academic collaborators in the UK NHS, Italy, and Kenya.

Where does the project lie on the Translational Pathway?

T1 – Basic Research          

Expected Outputs

• The project will produce high quality REF returnable 3*/4* publications and will provide the evidence base for large scale research council funding in a global priority area. Previous and current PhD students from TE and EH have all published one or several high-quality first-author papers, including Molecular Microbiology, PLoS Pathogens, Microbial Genomics and Nucleic Acids Research, and have all moved to postdoctoral positions or are working as a programmer in industry. Recent work from TE and EH on multidrug-resistant bacterial population dynamics has resulted in high-impact publications in Genome Biology, Nature Communications, Nature Microbiology and Microbial Genomics. The project will provide the unique opportunity to work on highly relevant clinical questions by a closely linked combination of computational and laboratory methods to understand the resistance dynamics of some of the most relevant Gram-negative opportunistic pathogens, in particular Escherichia coli and Klebsiella pneumoniae. There is clear scope for translational impact, with the project potentially providing evidence for improved or resistance blocking treatment regimens, and the potential to uncover diagnostic targets.  The student will furthermore be embedded in the larger collaborative network on opportunistic Gram-negative pathogens, which includes Prof. Corander (associate faculty at Wellcome Sanger Institute, faculty at University of Oslo and University of Helsinki), Dr. Cornick (group leader at UoL/MLW) and Abhilasha Karkey (associate professor Oxford University, leader of the Nepal clinical research unit).   This is a key strategic area for LSTM as evidenced by the recent appointment of TE on career track (2021)and EH who was recruited from the prestigious Wellcome Sanger Institute, rapidly passed career track, and was promoted to senior lecturer following her first 12-months tenure review.

Training Opportunities

Training in cutting edge pathogen bioinformatics will be provided by EH, who is a world leader in this field. Training in molecular techniques and microbiology will be provided by the TE lab, where these procedures are well established. The student will be able to attend courses on sequencing library preparation and nanopore sequencing ran by Oxford Nanopore and others. In general we will encourage the student to identify both internal and external training opportunities that are of interest and will support their attendance.

Skills Required

General microbiology and bioinformatics background would be advantageous

Key Publications associated with this project

Hubbard, A., Mason, J., Roberts, P., Parry, C., Corless, C., van Aartsen, J., Howard, A., Fraser, A., Adams, E., Roberts, A., Edwards, T. (2020). Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of blaTEM-1B_. Nature Communications. 11:4915 doi: 10.1038/s41467-020-18668-2

Edwards, T., Heinz, E., van Aartsen, J., Howard, A., Roberts, P., Corless, C., Fraser, A., Williams, C.T., Bulgasim, I., Cuevas, L.E., Parry, C.M., Roberts, A.P., Adams, E.R., Mason, J., Hubbard, A. Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections driven by multiple resistance mechanisms across diverse sequence types. (2022) Microbial Genomics.  Apr;8(4):000789. doi: 10.1099/mgen.0.000789

Lewis JM, Mphasa M, Banda R, Beale M, Heinz E, Mallewa J, Jewell C, Faragher B, Thomson NR, Feasey NA. Dynamics of gut mucosal colonisation with extended spectrum beta-lactamase producing Enterobacterales in Malawi. (2022) Nature Microbiology doi: 10.1038/s41564-022-01216-7.

Ellington MJ*, Heinz E* (*Equally contributing), Wailan A, Dorman M, Cain A, Henson S, Gleadall N, Brown NM, Woodford N, Parkhill J, Török EM, Peacock SJ, Thomson NR. Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center. (2019) Genome Biology. doi: 10.1186/s13059-019-1785-1.

Papp-Wallace, K.M. (2019). The latest advances in β-lactam/β-lactamase inhibitor combinations for the treatment of Gram-negative bacterial infections. Expert Opin Pharmacother. 20(17): 2169–2184. doi:10.1080/14656566.2019.1660772