Our Research
Research Themes
We approach this challenge from three interconnected perspectives:
(a) understanding how microorganisms acquire and disseminate antimicrobial resistance genes and other adaptive traits
(b) investigating how these acquired traits contribute to microbial survival and persistence
(c) exploring how bacteriophages can be harnessed as effective interventions against drug-resistant bacterial pathogens.
Our research combines structural biology, biochemistry, biophysics and microbiology to investigate the molecular machines responsible for these processes, with particular emphasis on large macromolecular assemblies and membrane-associated proteins.
Our research group is committed to understanding the molecular mechanisms underlying AMR, microbial evolution, adaptation and persistence, with the long-term goal of contributing towards the development of new strategies to combat infections caused by drug-resistant bacterial pathogens.
1. Horizontal Gene Transfer and Microbial Evolution
Horizontal gene transfer (HGT) is a fundamental driver of microbial evolution, enabling bacteria to acquire new genetic information and rapidly adapt to changing environments. Conjugation, one of the principal mechanisms of HGT, plays a major role in the dissemination of antimicrobial resistance genes, virulence determinants and other adaptive traits among clinically important bacterial pathogens.
Building on our previous structural studies of Type IV secretion systems (T4SS) involved in classical conjugation in Gram-negative bacteria, our current research focuses on understanding how Gram-positive bacteria employ distinct molecular machines to exchange genetic material.
Karsten Schneider ©
Structural and Functional Characterisation of Conjugative Type IV Secretion Systems in Staphylococcus aureus
Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is an important human pathogen responsible for a wide range of difficult-to-treat infections. Conjugative plasmids play an important role in the dissemination of antimicrobial resistance genes in this organism through specialised membrane-associated molecular machines known as Type IV secretion systems (T4SS).
Our laboratory investigates the conjugative machinery encoded by staphylococcal plasmids an established model for studying plasmid-mediated DNA transfer in Gram-positive bacteria. Unlike their extensively studied Gram-negative counterparts, the molecular architecture and mechanisms of Gram-positive conjugative systems remain poorly understood. Their operation within the distinctive cell envelope of Gram-positive bacteria raises important questions about how these molecular machines assemble and function.
Building on our expertise in the structural biology of bacterial conjugation, we aim to uncover the molecular organisation and functional principles of these systems, providing insights into the mechanisms underlying the dissemination of antimicrobial resistance in clinically important pathogens.
Molecular Mechanisms of Distributive Conjugal Transfer in Mycobacteria
Mycobacteria employ a distinctive form of horizontal gene transfer known as distributive conjugal transfer (DCT), which differs fundamentally from classical plasmid-mediated conjugation. Rather than transferring a single plasmid or continuous DNA segment, DCT facilitates the exchange and integration of multiple large chromosomal DNA fragments, generating highly mosaic genomes and extensive genetic diversity.
Our research focuses on understanding the structural and molecular basis of DCT, particularly the involvement of specialised Type VII secretion systems (T7SS), ESX-1 and ESX-4, which play important roles in mycobacterial genetic exchange. Although T7SS are well recognised for their roles in protein secretion, how these complex membrane-integrated molecular machines contribute to conjugative DNA transfer remains poorly understood.
We are particularly interested in determining the molecular architecture and functional organisation of the ESX-1 and ESX-4 secretion systems and understanding the overall mechanism of DCT. This includes investigating how secretion substrates are processed, recognised and recruited to the transport machinery, how their translocation across the mycobacterial cell envelope is mediated, and how the two secretion systems interact or coordinate their activities during genetic exchange between bacterial cells.
By integrating structural, biochemical and functional approaches, we aim to uncover the molecular principles governing this unusual form of conjugation, providing fundamental insights into mycobacterial genomic diversification, adaptation and evolution.
2. Bacteriophage Biology and Bacterial Defence Mechanisms:
Bacteriophages are viruses that infect bacteria and play a fundamental role in shaping microbial populations and driving bacterial evolution. Their ability to selectively recognise and eliminate bacterial pathogens has renewed interest in their potential as alternatives or complements to conventional antibiotics. However, the effectiveness of bacteriophages depends not only on their ability to infect susceptible bacteria but also on overcoming the diverse defence mechanisms bacteria have evolved to resist viral infection.
Our research investigates both sides of this evolutionary arms race: the molecular machinery responsible for phage infection and the bacterial defence systems that prevent successful phage replication.
Structural and Molecular Characterisation of Jumbo Bacteriophages Targeting Salmonella
Non-typhoidal Salmonella is a major foodborne pathogen responsible for substantial human and animal disease, with the increasing prevalence of multidrug-resistant strains creating an urgent need for alternative antimicrobial interventions. Our laboratory focuses on the structural and molecular characterisation of Salmonella jumbophages that infect Salmonella and forms part of a promising phage-based approach for controlling Salmonella infections in livestock.
Jumbo bacteriophages possess unusually large genomes and remarkably complex molecular architectures, comprising specialised assemblies responsible for virion stability, bacterial recognition, attachment and genome delivery. Understanding how these molecular machines are organised and function during infection is central to explaining the biological properties of these viruses and their potential for therapeutic applications.
Working alongside collaborators in bacteriophage biology and therapeutic development at the Becky Mayer Centre for Phage Research, we aim to establish a molecular understanding of SPFM10 architecture and infection mechanisms. These studies seek to provide a structural and mechanistic foundation for accelerating the characterisation and development of effective phage-based interventions against multidrug-resistant Salmonella.
Structural and Functional Characterisation of Bacterial Abortive Infection Systems
Non-typhoidal Salmonella is a major foodborne pathogen responsible for substantial human and animal disease, with the increasing prevalence of multidrug-resistant strains creating an urgent need for alternative antimicrobial interventions. Our laboratory focuses on the structural and molecular characterisation of Salmonella jumbophages that infect Salmonella and forms part of a promising phage-based approach for controlling Salmonella infections in livestock.
Jumbo bacteriophages possess unusually large genomes and remarkably complex molecular architectures, comprising specialised assemblies responsible for virion stability, bacterial recognition, attachment and genome delivery. Understanding how these molecular machines are organised and function during infection is central to explaining the biological properties of these viruses and their potential for therapeutic applications. Working alongside collaborators in bacteriophage biology and therapeutic development at the Becky Mayer Centre for Phage Research, we aim to establish a molecular understanding of SPFM10 architecture and infection mechanisms. These studies seek to provide a structural and mechanistic foundation for accelerating the characterisation and development of effective phage-based interventions against multidrug-resistant Salmonella.
3. Membrane Proteins Involved in Microbial Persistence:
Beyond understanding how bacteria acquire new genetic traits, we are equally interested in the functional consequences of these acquisitions, particularly how they contribute to microbial adaptation and persistence.
The ability of pathogenic bacteria to survive within their hosts depends on specialised mechanisms that enable them to withstand environmental challenges and host-mediated antimicrobial stresses. Membrane proteins play a central role in these processes by maintaining cellular homeostasis, regulating ion transport and protecting microorganisms against toxic conditions.
Our research investigates membrane transport proteins involved in microbial survival, particularly those associated with metal ion homeostasis in bacterial pathogens.
Structural and Functional Characterisation of Copper-Transporting ATPases in Staphylococcus aureus
Copper is an essential micronutrient but becomes toxic at elevated concentrations, a property exploited by the host immune system to combat bacterial infections. To withstand this antimicrobial stress, pathogenic bacteria have evolved specialised copper transport and resistance mechanisms that enable them to maintain cellular copper homeostasis. Our research focuses on the structural and functional characterisation of copper-transporting P-type ATPases in Staphylococcus aureus, particularly CopA, CopB and CopX, which contribute to bacterial copper homeostasis and survival. Of particular interest is the acquisition of additional copper-resistance determinants through horizontal gene transfer. Genes such as copX illustrate how acquired genetic traits can enhance bacterial tolerance to host-mediated antimicrobial stresses, providing a selective advantage under challenging conditions.
We aim to understand the molecular architecture, transport mechanisms and functional specialisation of Cu pumps and their contributions to microbial adaptation and persistence.
Strategy
Methods
Our goal is to understand how these biological processes work and to achieve this, we use a multi-disciplinary approach combining
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Structural biology: Crystallography, cryo-EM, cryo-ET
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Molecular biology and bacterial genetics
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Membrane-protein biochemistry
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Biophysics: Mass photometry, FRET, mass spectrometry
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Integrative structural biology: XL/HDX-MS, cross-linking
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Membrane biophysics: Electrophysiology, membrane potential, ion transport, proteoliposomes
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Microbiology: Conjugation, phage infection, bacterial defence assays
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Protein biochemistry: Enzymology, ATPase assays, protein–DNA interactions
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Computational biology: AI/ML modelling, molecular dynamics, bioinformatics
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Advanced microscopy: Live-cell imaging, confocal and fluorescence microscopy
David Goodsell @ Scripps ©
Environment
Our Community and collaborations
Horizontal Gene Transfer and Bacterial Conjugation
Our research on bacterial conjugation and mycobacterial horizontal gene transfer benefits from collaborations within the University of Leicester, including Molecular and Cell Biology (MCB), Respiratory Sciences and the Leicester Tuberculosis Research Group (LTRG), alongside collaborations with University College London (UCL), the U. Birmingham and international research partners.
Bacteriophage Biology and Bacterial Defence
Our bacteriophage research benefits from close collaborations with the Becky Mayer Centre for Phage Research and the Department of Genetics, Genomics and Cancer Studies at the University of Leicester. Our research on bacterial antiphage defence is further supported by collaborations with the Universities of Cambridge, Sheffield and Leeds, bringing complementary expertise in membrane biophysics, single-molecule fluorescence and structural mass spectrometry.
Membrane Proteins and Microbial Persistence
Our research on copper-transporting ATPases in Staphylococcus aureus is supported by collaborations within the University of Leicester, particularly through the MRC AIM programme, integrating expertise in bacterial physiology, metal homeostasis and structural biology.
Structural Biology and Biophysical Infrastructure
Our laboratory has access to state-of-the-art infrastructure at the Midlands Regional Cryo-EM Facility, including the Titan Krios and newly installed Glacios cryo-electron microscopes. We also benefit from the advanced X-ray crystallography, biophysics, microscopy and computational resources available through the Leicester Institute for Structural and Chemical Biology (LISCB), supporting structural and functional characterisation of complex biological systems.