Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent

BMC Microbiology

卷:19

Tim A. McAllister¹  Francis J. Larney¹  Rahat Zaheer¹  Rodrigo Ortega Polo¹  Shaun R. Cook²  Ron R. Read³  Steven M. Lakin⁴  Paul S. Morley⁴  Sherry J. Hannon⁵  Calvin W. Booker⁵  Gary Van Domselaar⁶ 

[1] Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre;

[2] Alberta Agriculture and Forestry;

[3] Cumming School of Medicine, University of Calgary;

[4] Department of Clinical Sciences, Colorado State University;

[5] Feedlot Health Management Services;

[6] National Microbiology Laboratory, Public Health Agency of Canada;

关键词: Microbiome;    Antimicrobial resistance;    Metal and biocide resistance;    Cattle production;    Wastewater;   

DOI  :  10.1186/s12866-019-1548-x

来源: DOAJ

【 摘 要 】

Abstract Background Comparative 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. Results Metagenomic 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. Conclusions This 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.

【 授权许可】

Unknown