Characterization of antibiotic resistance in bacterial communities: novel methods using next generation sequencing

Research Project, 2012 – 2015

The accelerated development of antibiotic resistance is one of the most urgent threats to human health. Bacteria become resistant to antibiotics by acquiring resistance genes through the process of horizontal gene transfer. Since antibiotics are naturally produced by many organisms, environmental bacterial communities contain a particular high diversity of resistance genes. Understanding the role of the environment as a reservoir for resistance genes and their routes of transfer is therefore vital. In this project we will develop novel tools for explorative analysis of resistance genes in bacterial communities. The tools are based on data generated by the next generation DNA sequencing and have therefore a high sensitivity and precision, even for less abundant genes. We will also develop tools for culture-independent characterization of resistance plasmids, which are the main vehicles for transmission of resistance genes between bacterial cells. The methods will be used to analyze data from environmental bacterial communities, both with and without antibiotic selection pressure, and the human microbiome. The project will generate novel insights into the development, promotion and spread of antibiotic resistance. The methods will have a great applicability in both basic and clinical microbiology as well as in metagenomics in general.

Participants

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Publications

Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake

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