Selection for antibiotic resistance in complex microbial communities

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It is becoming increasingly clear that the natural environment plays an important role in the evolution and dissemination of antibiotic resistance. This studentship will determine the mechanistic basis and significance of gene flow that underlies the abundance of antimicrobial resistance genes in bacteria inhabiting polluted natural environments such as downstream of waste water treatment plants (WWTPs). It is unclear whether increased prevalence of antibiotic resistant organisms associated with WWTPs is due to constant emissions of resistant organisms or whether bacteria such as multi-drug resistant E. coli persist and/or acquire resistance genes by horizontal gene transfer (HGT) in aquatic sediments under selection by environmental pollutants including antibiotic residues. This project will study selection for resistance in complex communities utilising mesocosm studies interrogated using culture and culture independent methods. The latter will include real-time PCR for enumeration of key marker genes and next generation sequencing (NGS) to determine the effects of single antibiotics, mixtures of different classes of antibiotic and field samples of polluted effluents on relative abundance of all known resistance genes. This knowledge will be used to support environmental policy development and environmental risk management.