Molecular epidemiology of antibiotic resistance in humans and animals

Antibiotic resistance is one of the largest and most pressing threats to human health. Understanding how antibiotic resistance emerges and spreads, and how we can detect this, is a key to developing strategies to overcome this threat. In addition to mutation, resistance can emerge through the transfer of resistance genes on plasmids, through transduction, or natural transformation. Resistance genes are often found in mobile genetic elements, such as transposons and integrons that can enhance their spread. Traditional methods to genotype bacteria such as PCR-based approaches or pulsed-field gel electrophoresis (PFGE) are being replaced by molecular approaches such as multi-locus sequence typing (MLST) and most recently whole genome sequencing (WGS). WGS is particularly powerful as it allows an assessment of the genetic relatedness of the bacteria, the specific resistance genes present, and the mobile elements that may be facilitating resistance gene spread or expression. Antibiotic resistance genes are frequently acquired from other bacteria, and can then be selected under antibiotic exposure. A One Health approach to antibiotic resistance, which considers the contribution of animals (such as those farmed for food) and the environment is a key to gaining a complete understanding of the epidemiology of antibiotic resistance.