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Metagenomics of antibiotic resistance

Thursday 17 January 2013

The term “metagenomics” was first coined in the late 1990s and describes the study of complete bacterial and viral ecosystems using modern genomics techniques. Over the past ten years metagenomic-based studies have greatly increased our functional understanding of the role that micro-organisms play in human health. The number of bacteria that inhabit a single human is estimated to be around 1014, which is at least ten times more than the number of cells of the human body. The gut is the most densely populated area of the human body and the highest bacterial load is reached in the colon where 1011 – 1012 bacteria/ml are present. These bacteria form an incredibly large reservoir of genetic information and in this research project we are tapping this reservoir to characterize the reservoir of antibiotic resistance (the “resistome”) that is associated with the human host. This reservoir can be of particular importance in the hospital as antibiotic resistance genes of human gut commensals may be selected for by antibiotic therapy and could eventually spread to pathogenic bacteria.

To determine the human resistome we are using culture-independent approaches. One approach that we are currently using starts with the isolation of DNA from feces. This DNA is then cloned into fosmids (a cloning vector that allows the introduction of large 40-kb DNA inserts) after which the resulting library is screened for antibiotic resistant phenotypes. Subsequently, inserts will be functionally characterized to determine which resistance genes are responsible for the observed phenotypes. We are also planning to expand these functional metagenomic approaches to microbial hosts other than the standard host E. coli to allow for screening of a larger variety of antibiotic resistance genes, including those that are active only against Gram-positive bacteria. We also aim to perform metagenomic sequencing to determine the phylogenetic composition and full gene repertoire of patient microbiota.

Standard molecular biology techniques: i.e. DNA isolation and electrophoresis, cloning, transposon mutagenesis, sequencing. High-throughput screening for antibiotic resistance. Bioinformatics.

6 or 9 months

Dr. Ir. Willem van Schaik, 088 75 565 35, w.vanschaik@umcutrecht.nl

Sommer et al,. 2009. Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora. Science 325:1128-1131
Wooley et al., 2010. A Primer on Metagenomics. PLoS Comput. Biol. e1000667