We use a combination of experimental evolution, genomics, molecular biology and biochemistry to understand the propensity for and mechanisms of antimicrobial resistance in the important human pathogen Clostridioides difficile. C. difficile is intrinsically resistant to many common antibiotics and infection normally follows an antibiotic-mediated insult to the gut microbiota that reduces colonisation resistance. Despite this connection between antibiotic chemotherapy and susceptibility to C. difficile infection (CDI), treatment of CDI typically relies one of small number of antibiotics. As these treatments cause further collateral damage to the gut microbiota, relapse or reinfection is a common problem.

In recent years we have studied the contribution of the C. difficile L,D-transpeptidase pathway to intrinsic beta-lactam resistance and the propensity for C. difficile to evolve resistance to the front-line antibiotic vancomycin.

The ability to form robust spores allows the Clostridia to survive incredibly harsh environmental conditions that would kill vegetative cells and, as strict anaerobes, is an absolute requirement for transmission between niches. The processes of sporulation and germination are complicated cell differentiation processes and are relatively poorly understood. In recent years we have applied transposon mutagenesis and TraDIS to identify the C. difficile genes required for sporulation, identified and characterised the cortex-specific PBP SpoVD and discovered an unsuspected link between biogenesis of the S-layer and sporulation. In collaboration with Prof Per Bullough, we have also characterised the C. sporogenes spore surface proteome and, using electron microscopy and atomic force microscopy, studied the structure of the exosporium.

We have a long running interest in the structure of phage and phage tail-like particles and the mechanisms by which these infect and kill bacterial cells.  We have collaborated with Sittinan Chanarat to study the endolysin from ϕHN16-1 and ϕHN50 and working with AvidBiotics (Now Phylum Biosciences) characterised a novel panel of engineered phage-tail-like particles (the Avidocins) that efficiently kill C. difficile. We identified that the C. difficile S-layer is the cell surface receptor for all of the phage RBPs used in creating the Avidocins and, more recently, in collaboration with Louis-Charles Fortier, determined that this is a common feature of phages the infect C. difficile.

In collaboration with Per Bullough, we have also developed a cryoEM pipeline for high-resolution structural analysis of phages and using this information we are using cryoEM combined with molecular microbiology we are dissecting the molecular basis of phage infection.