This project integrates synthetic biology, in vitro and in vivo experiments and mathematical modelling to predict and test the effectiveness and consequences of CRISPR-Cas9-mediated removal of antibiotic resistance from clinical pathogens in a realistic gut environment. The Van Houte lab has (1) a large collection of clinical isolates of carbapenem-resistant E. coli and K. pneumoniae, and vancomycin-resistant E. faecium, which will be subjected to CRISPR-Cas9 to remove drug resistance, and (2) a collection of conjugative elements and bacteriophages that will be tested as delivery vehicle for CRISPR-Cas9. We will assess how factors such as antibiotics levels, microbial community composition, delivery vehicle host range and transmission mode will influence the efficiency of CRISPR-Cas9 to remove resistance from clinical isolates.
