Constraints and Opportunities for Horizontal Gene Transfer in Bacterial Evolution

Project Information

HorizonGT

Grant agreement ID: 101077809

DOI

10.3030/101077809

EC signature date 1 February 2023

Start date 1 March 2023

End date 29 February 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 497 613,00

EU contribution

€ 1 497 613,00

Coordinated by

SERVICIO MADRILENO DE SALUD
Spain

Periodic Reporting for period 1 - HorizonGT (Constraints and Opportunities for Horizontal Gene Transfer in Bacterial Evolution)

Reporting period: 2023-03-01 to 2025-08-31

Summary of the context and overall objectives of the project

Bacteria have an extraordinary ability to exchange genetic material between individuals, a process known as horizontal gene transfer (HGT). This exchange fuels bacterial evolution, enabling microbes to rapidly acquire new traits, adapt to environmental challenges, and develop antibiotic resistance. However, not all gene transfer events are beneficial; sometimes, they burden bacteria with costly or harmful genes. Understanding why some HGT events succeed while others fail remains one of the major unanswered questions in evolutionary microbiology.

The HorizonGT project addresses this challenge by investigating the biological forces that shape the success of HGT. A central idea of the project is that the context in which genetic material is transferred —whether integrated into the host chromosome or carried independently by plasmids— profoundly impacts its evolutionary outcome. To explore this, the project aims to measure the fitness effects of thousands of gene transfer events using new, high-throughput experimental methods. Specifically, HorizonGT focuses on three main objectives. First, it systematically examines how plasmids, mobile genetic elements that often carry antibiotic resistance genes, influence bacterial fitness. Second, it studies how genes integrated into different regions of the bacterial chromosome affect host survival and competitiveness. Third, it investigates how HGT has shaped the evolution of major human pathogens, providing insights into how resistance and virulence traits emerge and spread.

The results of HorizonGT are expected to advance our understanding of bacterial evolution by offering a quantitative, mechanistic framework for HGT dynamics. Beyond fundamental science, this knowledge will help predict and potentially control the spread of antibiotic resistance, contributing to global health strategies against multidrug-resistant infections. By combining evolutionary microbiology, genomics, and synthetic biology, HorizonGT aims to open new research avenues and practical approaches to address one of the pressing challenges of modern medicine.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have performed a substantial amount of work since the beginning of HorizonGT. First, we developed and implemented a systematic strategy to investigate the biological factors determining the success of horizontal gene transfer (HGT) events. By performing a preliminary analysis of plasmid fitness effects across diverse bacterial hosts, we uncovered unexpected variability that prompted a deeper investigation into plasmid copy number (PCN). This led to the discovery of a universal scaling law linking plasmid size and PCN, providing a new framework for understanding plasmid evolution. A manuscript detailing these findings will be published in Nature Communications. Second, we deployed genome-wide high-throughput screens to map the genetic basis of plasmid fitness costs. These experiments revealed conserved host responses that modulate the fitness effects of plasmids. To interpret the rich datasets generated, we developed dedicated computational pipelines combining statistical modeling and functional annotation. Third, we found that the expression of β-lactamase genes was a major driver of HGT fitness costs. Following this research direction, we discovered that β-lactamase expression not only produces fitness costs, but it also induces collateral sensitivity to unrelated antibiotics such as colistin and azithromycin. This work, published in Nature Communications, provides new opportunities for combating antibiotic resistance.

In summary, the HorizonGT project has generated substantial advances in the understanding of bacterial evolution, plasmid biology, and resistance mechanisms. We have successfully developed innovative tools and concepts that are already producing a significant scientific impact.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

We have made several important advances beyond the state of the art in the field, such as:
- Discovering a universal scaling law linking plasmid size and copy number across bacterial taxa, providing a predictive framework for plasmid evolution.
- Revealing that β-lactamase expression is a dominant driver of plasmid fitness costs and induces collateral sensitivity to unrelated antibiotics.
- Developing high-throughput screens to systematically identify host genetic factors modulating plasmid fitness.
- Establishing new computational pipelines to interpret large-scale fitness and PCN datasets, combining statistical modeling and functional annotation.
- Advancing the understanding of how horizontal gene transfer shapes pathogen evolution by integrating clinical strain analysis with ecological modeling.