The role of toxin-antitoxin systems in plasmid host range in the framework of the current global antimicrobial resistance crisis

Toxin-antitoxin (TA) systems are small modular genetic elements, comprised of a toxin targeting basic cellular processes and the corresponding antitoxin. The antitoxin is less stable, so when the TA system is lost, the cells die as only the toxin remains. These TA systems were originally implicated in plasmid addiction; killing offspring cells that had lost the TA-containing plasmid, as the antitoxin is gradually degraded but the toxin is still active.

The recent epidemic of multidrug-resistance gene carrying plasmids has opened a lot of questions regarding their maintenance and way of spread, as it is clearly not random transmission. It is however poorly understood why some plasmids seem stably associated with some lineages of host bacteria, beyond what we currently understand about plasmid incompatibility. The candidate will have access to a large collection of bacterial isolates from relevant hospital diagnostic and environmental samples and will apply comparative genomics as well as functional analyses to determine how the presence or absence of TA systems impacts on different host cells. Recent studies have also detected a large number of orphan antitoxins, which could make bacterial cells more resistant to invading plasmids. We will use network inference to identify patterns in the toxin-antitoxin co-occurrences, characterising hubs and clusters in the inferred bipartite networks.

Preliminary data from AR's lab has also shown that TA systems, when expressed as a pair, have a significant fitness impact on the host. This project will address the impact of TA systems on the spread of antimicrobial resistance gene carrying plasmids. The first step will be detailed hypothesis formulation based on comparative genomics and presence/absence networks, which will then be confirmed with functional assays in the lab.  Transcription experiments under stress will be used to infer how TA systems, and the plasmids in general, influence and interfere with transcriptional regulatory networks. Further work will also incorporate reporter studies to identify novel TA systems from the genomes of the bacterial isolates under investigation, using a method recently implemented in the lab of AR (Tansirichaiya et al. 2019). 

Where does the project lie on the Translational Pathway?

T1 – Basic Research & T2 – Human/Clinical Research

Expected Outputs

The project is likely to result in a unique insight into plasmid dynamics (stability, movement and host range) which is dependent on TA systems present in the cell; both on and off the plasmid. The translational angle of this project is to use this information to determine control mechanisms of plasmids rather than the bacteria themselves. The project will produce high quality REF returnable 3*/4* publications and will provide data in a highly relevant area for follow-up funding at a global public health scale.

 

Recent work from the supervisory team on evolution, comparative genomics, multidrug-resistant bacteria and translational medicine has resulted in high-impact publications in the last 12 months including in Nucleic Acid Research, Genome Biology, Nature Communications and Scientific Reports, Lancet Infectious Diseases and EBioMedicine.

Training Opportunities

Training will be provided in bioinformatics (molecular evolution, comparative genomics, population genomics), statistics, epidemiology, microbiology and molecular biology, including sequencing (preparation of long-fragment DNA, MinIOIN sequencing). The student will furthermore be working with collaborators at the Biozentrum Basel (Switzerland; Dr. Alexander Harms), Lancaster University, the Wellcome Sanger Institute, and the Malawi-Liverpool Wellcome Centre (MLW). The student will have the opportunity to audit the Lancaster-based Masters level courses in Bioinformatics (BIOL445) and Statistical Genetics and Genomics (CHIC581).

Skills Required

The student should be comfortable working computationally as well as with bacterial isolates, and have an interest in comparative genomics and evolution.

Key Publications associated with this project

Harms et al. 2018 Molecular Cell.  Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

Dondelinger et al. 2013 Machine Learning. Non-homogeneous dynamic Bayesian networks with Bayesian regularization for inferring gene regulatory networks with gradually time-varying structure

Martino et al. 2019 PLoS ONE. Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient.

Horesh et al. 2018 Nucleic Acids Research. SLING: a tool to search for linked genes in bacterial datasets.

Tansirichaiya et al. 2019 Scientific Reports. Promoter activity of ORF-less gene cassettes isolated from the oral metagenome

LSTM Themes and Topics – Key Words

Resistance research and management