Antibiotic-Resistance Genes Are Ubiquitous in Soil Microorganisms

Richard T. Ellison III, MD

Nearly 3000 different antibiotic-resistance genes representing all major resistance mechanisms were detected in microorganisms from grassland and agricultural soil samples.

Recent studies have shown that the presence of antimicrobial-resistance genes (ARGs) long predated the clinical use of antibiotics (NEJM JW Infect Dis April 25 2012). New work on soil microorganisms has extended these observations, revealing a vast array of ARGs — most of them distinct from known ARGs in human pathogens.

Using functional metagenomics, researchers screened agricultural and grassland soil samples from two sites for the presence of ARGs active against any of 18 antibiotics from eight drug classes. The 2895 ARGs that they identified conferred resistance to 15 of the 18 antibiotics and represented all major resistance mechanisms. Only 15 of these ARGs had perfect amino acid identity to those recorded in the National Center for Biotechnology Information database; only 1 shared such identity with a gene from a pathogen. The ARGs varied by soil type and with the use of nitrogen fertilizers. Unlike ARGs in human pathogens that appear to spread easily among microorganisms by horizontal gene-transfer mechanisms such as transposases and integrases, only 0.42% of the soil ARGs appeared to have flanking mobility elements that would allow such transfer.

Citation(s):

Forsberg KJ et al. Bacterial phylogeny structures soil resistomes across habitats. Nature 2014 May 21; [e-pub ahead of print].

Sommer MO.Barriers to the spread of resistance. Nature 2014 May 21; [e-pub ahead of print].