Cattle manure is a potential reservoir of antibiotic resistance genes (ARGs), and the application of manure to agricultural soils may increase the abundance and diversity of ARGs in soil. A thorough understanding of ARGs in manure can help assess the risk of ARGs and subsequently to control their proliferation in the environment. Current metagenomic sequencing methods for ARGs analysis target total genomic DNA that includes both resistant and nonresistant bacteria and hence suffer from low recovery rates of ARGs. The risk assessment is based on relative abundance (i.e, ARGs/16s and ARGs reads/total reads) other than absolute abundance. This study tests a new approach for quantitative AMR risk assessment in cattle manure by integrating AMR bacterial isolates libraries with metagenomic sequencing. This new approach has the following components: (1) establish large isolate libraries of particular fecal bacterial species (e.g. <i>E. coli</i>), (2) determine the antibiotic resistance patterns of the isolate libraries, (3) conduct metagenomic sequencing and the resistance isolate mixtures, and (4) conduct bioinformatic detection of ARG. Currently, an <i>E. coli</i> isolate library has been established, their AMR phenotypes are being determined, and metagenomic sequencing will be conducted soon.

Integration of antimicrobial resistant bacterial isolate libraries and metagenomics sequencing for quantitative antimicrobial resistance (amr) risk assessment in cattle manure

2019 Fall National Meeting

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