Abstract
Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide–lincosamide–streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause–effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms’ records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the “resistance potential” of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.
Highlights
Antimicrobial resistance (AMR) is an important worldwide public health issue (Penders et al, 2013; WHO, 2014)
This study demonstrated that resistomes in beef feedlot and dairy cattle operations were different between farms with distinct production practices (CONV vs. RWA)
This agrees with results reported by Vikram et al (2017) who found slight differences in the fecal resistome of CONV and RWA cattle, it cannot be discounted that between-farm variability inherent to resistomes may have influenced the differences measured in this study
Summary
Antimicrobial resistance (AMR) is an important worldwide public health issue (Penders et al, 2013; WHO, 2014). AMR in bacterial communities has been investigated using cultures of indicator organisms such as Escherichia coli, Campylobacter, and Salmonella (Luangtongkum et al, 2006; Sapkota et al, 2014; Zwonitzer et al, 2016), or by amplification of a limited number of antibiotic resistance genes (ARGs; Cohen et al, 2012; Guarddon et al, 2014; Beukers et al, 2018) detected via polymerase chain reaction (PCR) methods. Increased understanding of the resistome in different livestock farms will aid our understanding of AMR ecology and discussing of effective production practices to limit ARGs dissemination from animals to humans
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
