RESUMO
Antimicrobial resistance in pathogenic bacteria is one of the preeminent concerns for the future of global health. There is a dose-dependent relationship between antimicrobial use (AMU) and the prevalence of antimicrobial-resistant pathogens. As most AMU in Canada is related to animal agriculture, there is a need to reduce overall AMU, which could be accomplished through surveillance of AMU in animal agriculture, including the dairy industry. The objective of this study was to quantify AMU on dairy farms across Canada. This study had two parts: a description of data collected in 2019-2020, and a meta-analysis comparing this data to previous estimates of AMU in the Canadian dairy industry. The first included a garbage can audit (GCA) on 107 farms in four Canadian provinces (British Columbia, Alberta, Ontario, and Nova Scotia) in 2020; AMU data were converted to the dose-based metrics of defined course doses (DCD) and defined daily doses (DDD). Mixed-effect linear models were fit to determine the relationship between province and use of different classes of antimicrobials. On average, for every 100 animals on the farm, 117 DCD of antimicrobials were administered per year (IQR: 55, 158). These treatments amounted to 623 DDD / 100 animal-yr (IQR: 302, 677 DDD/100 animal-years). Penicillins were the most used class of antimicrobials, followed by first-and third-generation cephalosporins. Farms in Ontario used more third-generation cephalosporins than other provinces. The second part of this study compared AMU in 2020 to previously reported Canadian studies through a meta-analysis. A GCA was conducted in 2007-2008 in Alberta, Ontario, Québec, and the Maritime provinces (Prince Edward Island, New Brunswick and Nova Scotia); another GCA was conducted in Québec in 2018. Overall, AMU was lower in 2018-2020 than in 2007-2008, with the exception of third-generation cephalosporin use, which increased.
RESUMO
Bulk tank milk (BTM) is regularly used for surveillance on dairy farms for disease conditions such as mastitis and Johne's disease. In this study, we used 16S rRNA sequencing and bait-capture enrichment to characterize the microbiota and resistome of BTM, and investigate potential differences between the cream or pellet fractions. A total of 12 BTM samples were taken from 12 Prince Edward Island dairy farms, in Atlantic Canada, in duplicates. The DNA was analyzed by high-throughput sequencing of the 16S rRNA gene and a suite of antimicrobial resistance (AMR) genes. Target-capture enrichment of AMR genes was conducted before shotgun sequencing. The bioinformatics pipelines QIIME 2 and AMR++ were used for microbiota and resistome analysis, respectively. Differences between microbiotae were evaluated qualitatively with nonmetric multidimensional scaling and quantitatively with permutational ANOVA of UniFrac distances. A total of 47 phyla were present across the BTM samples. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the most abundant phyla. At the genus level, Corynebacterium, Acinetobacter, Lactobacillus, and Turicibacter were the most abundant. There was no significant difference in the Faith's phylogenetic diversity between the cream and pellet fraction. Faith's phylogenetic diversity differed marginally by stall type. There were 10,217 hits across 80 unique AMR genes, with tetracycline resistance being the most common class.
