Award details

Understanding the pathway to multidrug resistant bacterial pathogens

Reference	BB/W020602/1
Principal Investigator / Supervisor	Professor Alan McNally
Co-Investigators / Co-Supervisors	Professor Samuel Sheppard
Institution	University of Birmingham
Department	Institute of Microbiology and Infection
Funding type	Research
Value (£)	873,991
Status	Current
Type	Research Grant
Start date	01/11/2022
End date	31/10/2025
Duration	36 months

Abstract

The emergence of MDR pathogens is a global challenge that must be addressed. However, MDR evolution rests upon a paradox. On the one hand, it promotes adaptation by conferring novel functionality on the recipient genome allowing proliferation in the presence of antibiotics, on the other, it introduces disharmonious genes or gene-combinations that may be discriminated against by selection. Therefore, MDR emergence is a complex process involving potentiating and accommodating changes that modify the co-adapted genomic landscape. Our program will identify novel genomic and functional variations that promote AMR emergence in enteric organisms. Extending pilot work to contemporary isolate collections of phylogenetically diverse E. coli, we will test hypotheses that: (i) Selection on key pathway genes underpins the evolution, emergence, and expansion of pandemic MDR clones. (ii) Mutations in core metabolism genes potentiate antimicrobial resistance leading to MDR plasmid acquisition (iii) MDR plasmids trigger expression of core metabolism genes to potentiate resistance and allow cost-free plasmid integration and maintenance. First we will employ novel genome-wide covariation analyses to characterize signatures accompanying MDR emergence. Second, we will statistically link these signatures with AMR phenotypes (e.g. tolerance, persistence) using genome-wide fitness profiling (Tn-Seq) to quantify the contribution of these changes to MDR emergence. Finally, the reproducibility and causal role of potentiating changes will be validated by combining comparative genomics with experimental evolution to reconstruct the pathway to MDR. By explaining the steppingstones to MDR in diverse E. coli from clinical samples, and supporting this with species-wide comparison, our findings will be readily translatable to real-world applications. In particular, enhancing phenotypic and genotypic surveillance programs for enteric bacteria in public health.

Summary

Infections caused by gram negative bacteria are among the most significant challenges in modern health care. The problem is exacerbated by a decline in antibiotic effectiveness and the emergence of new mechanisms of resistance. Mitigating this escalating problem depends upon detailed understanding of the genotypic and phenotypic changes that occur on the pathway to multidrug resistance (MDR). Widespread next-generation sequencing is now a routine component of pathogen surveillance and has confirmed the presence of antimicrobial resistance genes and MDR plasmids in global pandemic clones. However, little is known about the evolutionary 'stepping stones' that lead to the emergence of MDR. Understanding these could help with identifying early warning signs and public health interventions. We will investigate the underlying evolutionary mechanisms that give rise to MDR in bacteria. Unlike other studies, that focus on the presence of well known resistance genes - such as those linked to Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase enzymes, we will identify the series of evolutionary events that underpin MDR acquisition. Specifically, we will investigate: (i) genes that confer low level resistance - the stepping stones to MDR; (ii) potentiating genes that may predispose certain strains to plasmid acquisition; (iii) accommodating genetic change that maintains MDR plasmids; (iv) if divergent strains have convergent evolutionary steps towards MDR; (v) the repeatability of MDR emergence. To address these question areas we will take an interdisciplinary approach, analysing very large diverse E. coli isolate collections. Combining comparative and functional genomics approaches with new bioinformatics methods and in vitro experimental evolution assays, we will characterize the evolutionary events and genetic changes that underpin the emergence and spread of pandemic MDR E. coli - the most common global cause of urinary tract infections and bacteraemia. First, wewill identify genetic changes that covary with MDR. Second, we use genome-wide fitness profiling to investigate the genes and networks that potentiate or accommodate AMR phenotypes (tolerance, persistence etc.). Finally, we will investigate the reproducibility of evolution using an experimental evolution framework to test the repeatability of evolution in multiple genetic backgrounds of both clinical isolates and reference strains. This will identify predisposing factors and potentiating mutations that confer low level resistance and facilitating MDR plasmid acquisition and maintenance. This project will increase knowledge of the critical problem of MDR by identifying genetic changes underlying the emergence of resistance in pathogens responsible for some of the most common and serious systemic bacterial infections. Because we will characterize genetic changes in isolates from contemporary (real-world) infections, as well as across species diversity, we can be confident that our findings will be relevant to the ongoing battle against emergent MDR bacteria. In particular, helping design new laboratory testing for surveillance, outbreak risk models and targeted interventions.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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