Abstract
BackgroundComparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage.ResultsMetagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance.ConclusionsThis study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.
Highlights
Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking
For sewage influent (SI), 24.5% of the sequence reads were associated with bacteria and archaea, whereas soil, catchment basins (CB) and fecal samples (FC) had a much smaller proportion of prokaryote-associated reads (3.4, 4.5 and 2.1%, respectively), as revealed by the taxonomic classification via Kraken
Comparison of normalized data across all samples supported the largest abundance of microbial taxa reads in SI, being 6.2, 6.7, and 2.4 fold higher than in FC, CB and soil, respectively (Fig. 1)
Summary
Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. Antimicrobials have played an important role in controlling bacterial infectious diseases in both humans and animals. Bacteria residing in the bovine gastrointestinal tract may become resistant to these antibiotics and, once released into the environment, they may transfer antimicrobial resistance (AMR) genes (ARGs) to other bacteria including potential human pathogens [4, 5]. Residual antibiotics may enter the environment through runoff from manure, where they may select for antimicrobial resistant bacteria [6, 7]. It is not surprising that for almost every livestock-associated bacterial pathogen, resistance to at least one antimicrobial from each antimicrobial class has been reported [8]
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