Abstract
BackgroundAntimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures.ResultsMicrobial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types.ConclusionsAntimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.
Highlights
Sequencing information In this study, a total of 33 metagenomic libraries inclusive of cow feces, manure, lagoon, and soil samples collected from 3 conventional and 3 organic farms in southeastern Pennsylvania were analyzed for their composition of microbial communities, distribution of antimicrobial resistance genes (ARG), and bacterial hosts carrying ARG
The average number of sequence reads per sample was 29,346,035 A total of 9123 ARG were identified by comparing quality-filtered sequence reads to the MEGARes2 database
Community clustering patterns based on microbiome and resistome profiles Based on nonmetric multidimensional scaling (NMDS) analysis (Fig. 1), microbial communities clustered by sample type irrespective of farm type
Summary
The “critically important” category includes medications such as ceftiofur, a third-generation cephalosporin used in cattle to treat conditions such as bovine respiratory disease; this drug is considered critically important in human medicine because it is one of the few reliable treatments for infection with Escherichia coli and Salmonella spp. It is apparent, that the use of antimicrobials in livestock has the potential to impact human health
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