Editors' ChoiceMicrobiology

Antimicrobial Drug Resistance in All Four Corners of the Earth

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Science Translational Medicine  11 Jun 2014:
Vol. 6, Issue 240, pp. 240ec103
DOI: 10.1126/scitranslmed.3009591

The discovery of antibiotics in the early 20th century was one of the most important medical advances in history. However, humans came rather late to the use of antibiotics. Longer than the human species has existed, microorganisms have generated their own antibiotics to provide a survival advantage against other competing or infecting microorganisms. In turn, antibiotic resistance mechanisms evolved as a countermeasure. Now, Nesme et al. reveal just how widespread and diverse those antibiotic resistance mechanisms are.

Taking advantage of publicly available data, the authors identified 71 shotgun sequencing metagenomes (collective genetic material in an environmental sample) from a variety of sources, including Antarctic lakes; Arctic snow; ocean water; soil from multiple locations; air filters; sludge; feces of human, mouse, cow, and chicken; as well as other sources. Then, they cross-referenced these metagenomic sequences to the Antibiotic Resistance Database, which describes ~3000 different amino acid sequences conferring antibiotic resistance. This allowed the authors to define the abundance, diversity, and specific types of antibiotic resistance gene determinants (ARGD) in each metagenome.

Every sampled environmental metagenome included ARGD sequences. The abundance of such sequences ranged from 0.05% in chicken gut to 5.6% in human feces. Moreover, the diversity of ARGD sequences was also highly variable. About 1% of sequences in the Antibiotic Resistance Database were identified in cow gut. In contrast, nearly 33% of these sequences were identified in soil from a research park in the United Kingdom. Human feces had an intermediate diversity, comprising 13% Antibiotic Resistance Database sequences. Next, the authors defined the different types of resistance-imparting sequences. Most common were sequences encoding multidrug resistance efflux pumps, accounting for nearly 60% of global abundance as measured in the 71 metagenomes; then came vancomycin resistance at 17%, β-lactam resistance at 9%, and tetracycline resistance at 7% of global abundance.

This study highlights the global extent of naturally occurring antibiotic resistance genes, even where there has been no clinical use of antibiotics. Given that this pool of antibiotic resistance genes cannot be depleted, the focus turns to understanding the role that such genes play in microbial physiology and ecology, limiting their dissemination and minimizing antibiotic-induced selection.

J. Nesme et al., Large-scale metagenomic-based study of antibiotic resistance in the environment. Curr. Biol. 24, 1096–1100 (2014). [Abstract]

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