Background
The Antibiotic Resistance Crisis
Antibiotic resistance is one of the biggest threats to global health, driven predominantly by the overuse and misuse of antibiotics and the unavailability of newer drugs. Many antibiotics which once transformed medical sciences have been rendered useless following the emergence of multidrug resistant pathogenic bacterial strains. When new candidate antibiotics are developed, preclinical evaluations include assessing the likelihood and rate of bacteria evolving resistance to the antibiotic in vitro. If the resistance rate is too high, further development of the antibiotic may be terminated. Traditionally, to investigate the rate of resistance emerging, bacteria are exposed to the candidate antibiotic at a relatively high concentration which only permits growth of resistant mutants. This approach, however, ignores a key facet of bacterial evolution - horizontal gene transfer. Through this mechanism bacteria can readily transfer genes between one another, allowing access to a collective DNA pool termed 'the resistome'. To more accurately model this scenario, researchers have begun functionally screening metagenomic DNA to assess the prevalence of antibiotic resistance genes in the environment and resistome.
Our Approach
The Ackerley lab has developed a novel technique that promotes high-level expression of metagenomic DNA fragments in E. coli hosts. This is achieved by preparing metagenomic libraries with a proprietary restriction enzyme that enriches for the capture of full open reading frames (starting from the start codon) placed in close proximity to a strong E. coli promoter and ribosome binding sequence. This method of library creation greatly increases the likelihood that captured genes will express at high levels in the host bacterium. The Ackerley lab is interested in identifying strong, mature resistance elements as well as weaker, primordial elements. Investigation of the latter comprises our study of the 'primordial resistome'; whereby weak elements will be artificially evolved in the lab using directed evolution to model whether they are likely to promote future resistance. By identifying the pattern of mutations that could transform a primordial resistance gene into a strong resistance element, we can hypothesise interventions which may slow the emergence of resistance.
Above: an example workflow for screening soil metagenomic libraries for identification of novel antibiotic resistance elements
Research Projects
Metagenomic screening for primordial antibiotic resistance genes