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    Basic science

    Can the gut microbiota contribute to the emergence of antibiotic resistance?

    Forslund K, Sunagawa S, Roat Kultima J, et al. Country-specific antibiotic use practices impact the human gut resistome. Genome Res Published Online First: 8 April 2013. doi:10.1101/gr.155465.113

    The human gut microbiota is considered a reservoir for antibiotic resistance genes (ARGs). With increasing concerns over inappropriate antibiotic usage both in medicine and agriculture, the development of bacterial resistance mechanisms is of great concern. These resistance mechanisms can be transferred via mobile genetic elements such as plasmids or transposons and therefore horizontal transfer within the gut is likely. To date there have been limited attempts to determine the antibiotic resistance potential of the human gut microbiota. This is in spite of the insatiable demand for delineation of the gut microbiome in almost every conceivable disease state—many of which require antibiotic intervention. This recent study from Germany has for the first time defined the content and variation of the antibiotic resistance potential across large-scale datasets from across the world, in order to document geographical differences in resistance to 68 classes of antibiotics. Using previously collected metagenomic data from 252 faecal metagenomes obtained from MetaHIT, HMP and a collection of smaller studies, they were able to show that samples from southern Europe (Spain, Italy and France) contained higher levels of resistance genes compared to Denmark, the US and Japan. Resistance was detected in 50 of the potential 68 antibiotic classes, with an average of 21 per patient sample. Resistance genes were more frequently detected from antibiotics used in animals and particularly those that have been in use for a longer period of time. The geographic differences largely coincided with veterinary and human antibiotic usage data (where available). Assessment of ARG persistence was also documented in a small subset of patients who had faecal samples collected over an extended period. This demonstrated …

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