Friday, 16 June 2017 15:12

Agricultural antibiotic usage selects for antibiotic-resistant soil bacteria

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Published in mBiosphere

Antimicrobial resistance is a huge issue in the clinical setting, where the use of many antimicrobial therapies selects for resistant strains. However, selection for resistant microbes doesn’t only occur in healthcare clinics or hospitals – many environmental practices can select for resistance, too. A new Applied and Environmental Microbiology report demonstrates that farm practices can directly lead to development of novel antibiotic resistance mechanisms.


AppEnvMicro: Functional metagenomics reveals novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming.


The study, led by senior author Edward Topp, investigated the role of agricultural practices on selection for antibiotic resistance among soil bacteria. Over the course of the study, the research team sampled the bacterial soil for antibiotic-resistance genes (ARG) by functional metagenomics. Escherichia coli carrying DNA extracted from these soil microbes was tested for growth with 12 compounds from six antibiotic classes. The team observed 34 new ARGs, including several previously unidentified.

Antibiotic resistance mechanisms are commonly found in environmental microbes; the first bacterial-derived antibiotic was isolated from the soil fungus Penicillium. The resistance mechanisms found in soil metagenomic material included both well-characterized resistance determinants and a novel gene with an unknown mechanism conferring macrolide resistance.

Macrolides are a broad-spectrum antibiotic with rising levels of resistance observed in recent years. The drug works by binding the bacterial ribosome to interfere with protein synthesis, and resistance generally involves ribosome-associated mutation, drug modification, or efflux pump overexpression. The small, proline-rich peptide identified in this study conferred resistance through a novel, yet-to-be-identified mechanism.

The link between antibiotic use in livestock (particularly prophylactic use for growth-promoting purposes) is fairly well established, which is one reason this practice has been discontinued in the United States and Canada, where the study was conducted. The current study also avoided using this practice. However, other agricultural methods, such as application of fertilizer or wastewater, can introduce low levels of antibiotics or other stressful environments that select for resistant bacterial growth.

This study highlights the importance of environmental microbes as a reservoir of antimicrobial determinants. While this study focuses on potential selective pressures of agricultural practices, many environmental conditions can select for drug resistance, including hospital and municipal sewage, factory waste from antibiotic-production facilities, and even specific weather patterns. Understanding the potential resistance mechanisms that exist in the environment through studies such as these may help scientists be better prepared if a new mechanism jumps into the clinical setting.

Last modified on Friday, 16 June 2017 15:33
Julie Wolf

Julie Wolf is the ASM Science Communications Specialist. She contributes to the ASM social media and blog network and hosts the Meet the Microbiologist podcast. She also runs workshops at ASM conferences to help scientists improve their own communication skills. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.

Julie earned her Ph.D. from the University of Minnesota, focusing on medical mycology and infectious disease. Outside of her work at ASM, she maintains a strong commitment to scientific education and teaches molecular biology at the community biolab, Genspace. She lives in beautiful New York City.