Abstract

Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.

Highlights

  • The emergence of antimicrobial resistant (AMR) bacteria is one of the most important public health challenges worldwide [1]

  • The number of AMR genes differed between tested animals, and in general, higher levels of AMR genes were observed in food-producing animals than in wildlife

  • We applied metagenomics to investigate the epidemiology of AMR in various animal species

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Summary

Introduction

The emergence of antimicrobial resistant (AMR) bacteria is one of the most important public health challenges worldwide [1]. Estimates assume that AMR annually triggers more than 700,000 deaths worldwide [2, 3]. In 2015, infections caused by multidrug-resistant bacteria have led to 33,000 deaths in the European Union (EU) and the European Economic Area (EEA) [4]. Recent report of Centers for Disease Control and Prevention points up to 35,000 fatal cases per year due to AMR in the United States [5]. Estimated attributable AMR costs in the EU alone reach 1.5 billion EUR annually [2]. The severe economic consequences encompass productivity losses in agriculture and animal production [2, 3]

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