Abstract: In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota (‘the gut resistome’). Here, I will discuss different methods to profile the gut resistome, including shotgun metagenomic sequencing, functional metagenomics and high-throughput qPCR methodologies and I will present recent studies of my group into the gut microbiota and resistome of critically ill patients that receive intensive antibiotic therapy.

In addition, I will present recent work on the evolution of colistin resistance in Escherichia coli and Klebsiella pneumoniae. Due to the emergence and spread of carbapenem resistance, colistin has become an antibiotic of last resort. It is uniquely active against Gram-negative bacteria, due to its mode-of-action, which involves the destabilization of the outer membrane (OM) by interacting with the lipid A moieties of lipopolysaccharide (LPS) in the OM. We have studied the evolution of colistin resistance in clinical E. coli isolates, and through in vitro evolution experiments with K. pneumoniae and have identified mutations contributing to colistin resistance by whole-genome sequencing. We are currently studying the impact of colistin resistance on fitness, virulence characteristics and susceptibility to other antibiotics.