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ARS Home » Research » Annual Report on Science Accomplishments » FY 2020 » Combating Antimicrobial Resistance

Combating Antimicrobial Resistance

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ARS research elucidates the factors associated with antimicrobial resistance (AMR) in agricultural settings and develops tools and alternatives to antibiotics that mitigate AMR for the benefit of human, animal, and ecosystem health. Antimicrobials such as antibiotics will remain an essential tool for treating animal and human diseases, though the growing prevalence of resistant bacteria has garnered global concerns over the prudent use of antibiotics in animals. The following FY 2020 accomplishments highlight ARS advances in optimizing the use of and reducing the need for antibiotics in agriculture.

Prevalence of mobile colistin resistance in U.S. animal-origin food. Colistin, also known as polymyxin E, is a last-resort antibiotic against drug-resistant Gram-negative bacterial infections. Recently, a mobile colistin resistance gene, mcr-1, was discovered in clinical and animal samples. The prevalence of mcr-1-mediated colistin resistance has never been investigated in U.S. animal products. To fill this gap, ARS researchers in Albany, CA, screened more than 5,000 domestic food samples (chicken rinse, ground beef, beef trim, poultry, raw pork, and catfish) randomly collected by the USDA Food Safety Inspection Service for the presence of mcr-1 using a novel method developed by ARS that combines an enzyme-linked immunosorbent assay with real-time polymerase chain reaction methods. The screening data revealed a very low prevalence (0.02 percent) of the mcr-1 gene in tested samples. Subsequent whole genome sequence analysis on the single positive isolate revealed that the mcr-1 gene resided on an IncI2 plasmid. This study was the first systemic and large-scale investigation of mobile colistin resistance in U.S. food animal products, and the information will be important for trade-related food safety risk assessments.


House flies collected in agricultural settings carry antimicrobial-resistant bacteria. House flies are primary pests of confined livestock operations such as dairies, and due to their close associations with humans, are nuisance pests in domestic settings. Adult flies frequent microbe-rich substrates such as garbage dumpsters and animal manure, where they encounter and ingest bacteria during feeding and reproduction. To assess human and animal health risks, bacteria were enumerated from whole flies, identified to species, and tested for susceptibility to 14 antimicrobials. Both male and female flies carried antimicrobial-resistant (AMR) bacteria: 36 of 38 isolates (95 percent) were resistant to more than one antimicrobial, 33 were multidrug-resistant (MDR); and 24 isolates were resistant to more than 4 antimicrobials. These results emphasize the role flies may play in harboring and disseminating bacteria, including AMR and MDR strains and potential pathogens that pose a risk to human and animal health. The results add to the growing evidence implicating flies as major players in disease ecology, epidemiology, and the dispersal of AMR genes.

New economical and efficient strategy to remove antibiotics from wastewater. Understanding the removal mechanism of antibiotic compounds and antibiotic resistance determinants in agricultural systems is a global challenge that is important in the protection of human health. An ARS researcher from Riverside, CA, and collaborator from University of California, Riverside, designed and tested a layered environmental media system (consisting of gravel, sand, soil, and a “soil plus biochar” combination) through which antibiotic-laden water was pumped. Overall removal efficiencies of four tested antibiotics—amoxicillin, cefalexin, sulfadiazine, and tetracycline—were 81, 91, 51, and 98 percent, respectively. If the exposure time was lengthened, the removal efficiency was increased, especially for amoxicillin and cefalexin. Overall, the results from this lab-scale proof of concept system indicate the potential of the system for antibiotic removal from wastewater, and highlight ways in which removal efficacy improvements may be scalable for broad applicability. The results of this study will be used by wastewater treatment facilities, the World Health Organization, researchers, and other local municipalities in many developing countries.

Novel antibiotic-producing bacteria discovered on squid eggs. Discovery of new antibiotics is increasingly critical to combat the dramatic rise in multidrug resistant bacteria. Scientists at the University of Connecticut, the University of Texas-San Antonio, and the University of Florida, in collaboration with an ARS scientist in Peoria, IL, characterized several antimicrobial compounds produced by bacteria in the jelly coat of squid eggs. These antimicrobial compounds prevent overgrowth by fungi and other microorganisms on the eggs. Both experimental and analytical approaches revealed that multiple bacteria associated with the eggs, and chemical extracts of those bacteria, inhibited growth of the pathogenic mold Fusarium keratoplasticum and yeast Candida albicans. The discovery of novel antimicrobials is critical to promoting public health globally because many antibiotics available to clinicians cannot be administered to patients with life-threatening multidrug resistance infections.