Resistome diversity in cattle and the environment decreases during beef production

  • Noyes N
  • Yang X
  • Linke L
  • et al.
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Abstract

Antimicrobial resistant determinants (ARDs) can be transmitted from livestock systems through meat products or environmental effluents. The public health risk posed by these two routes is not well understood, particularly in non-pathogenic bacteria. We collected pooled samples from 8 groups of 1741 commercial cattle as they moved through the process of beef production from feedlot entry through slaughter. We recorded antimicrobial drug exposures and interrogated the resistome at points in production when management procedures could potentially influence ARD abundance and/or transmission. Over 300 unique ARDs were identified. Resistome diversity decreased while cattle were in the feedlot, indicating selective pressure. ARDs were not identified in beef products, suggesting that slaughter interventions may reduce the risk of transmission of ARDs to beef consumers. This report highlights the utility and limitations of metagenomics for assessing public health risks regarding antimicrobial resistance, and demonstrates that environmental pathways may represent a greater risk than the food supply.When bacteria become resistant to antibiotics, it becomes difficult or impossible to treat infections in both people and animals. Antibiotic resistance is a growing problem, and many fear a “post-antibiotic era” in which common infections become life threatening.In order to slow the spread of antibiotic resistance, it is important to understand how and where this resistance develops. In general, using antibiotics increases the likelihood that bacteria will develop resistance. Therefore, locations where antibiotics are commonly used – such as hospitals, long-term care facilities, livestock facilities (such as feedlots) and crop production areas (such as orchards) – may help antibiotic resistance to develop and spread. However, it is largely unknown how much each location promotes the emergence of antibiotic-resistant bacteria.Until recently, we have only been able to investigate how resistance develops in bacteria grown in a laboratory; or to look for a handful of specific resistance genes in a sample of bacteria collected from people, animals or the environment. Fortunately, a technology called next-generation sequencing now allows us to look at all the resistance genes within all the bacteria in a sample. This may help us to improve our understanding of how and where resistance develops and spreads.Noyes et al. have now used next-generation sequencing to describe the antibiotic resistance potential (known as the “resistome”) found in various types of samples collected from feedlots and slaughterhouses involved in producing beef. This showed that the number of different resistance genes in the samples decreased while cattle were in the feedlot and during the slaughter process. Several groups of resistance genes that were detected when the cattle first arrived in the feedlot were not detected at all at the end of the feedlot period. However, some resistance genes were detected throughout the feedlot period, and these tended to be resistance genes that allow the bacteria to evade the same antibiotics that were used in the cattle. In addition, no resistance genes of any type were detected in the samples collected after the cattle had been slaughtered.As well as providing insights into the resistome of beef production, Noyes et al.’s study also highlights the fact that we need to develop a deeper understanding of the data that come from next-generation sequencing. This may involve developing new laboratory techniques and creating new methods to analyze such data.

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Noyes, N. R., Yang, X., Linke, L. M., Magnuson, R. J., Dettenwanger, A., Cook, S., … Belk, K. E. (2016). Resistome diversity in cattle and the environment decreases during beef production. ELife, 5. https://doi.org/10.7554/elife.13195

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