Evaluation of Antibiotic Resistance Gene Profiles As a Microbial Source Tracking Tool.

Antibiotic use in the livestock industry is suspected to be a major contributor of emerging antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment.  Considering that significant amounts of managed manure from commercial facilities is applied to land, the risk of ARGs and ARB reaching nearby surface waters poses significant concerns for public and environmental health. The goal of this study was to use ARG profiles to identify the host sources of E.coli isolates (n=200) collected from Six Runs Creek, a creek near a commercial swine facility in Sampson County, NC.  ARG profiles were generated from E.coli isolates (n=808) from swine lagoon liquid and feces from swine, cattle, and wildlife sources. All isolates were evaluated for the presence/absence of aadA, strA, strB, tetA, tetB, tetC, sul1, sul2, sul3, and Aac3IV genes.  Removal of duplicate ARG profiles and application of an 80 % certainty of correct classification threshold to the isolates from known hosts resulted in a library composed of 157 isolates with an average rate of correct classification (ARCC) of 80.3%.  An average of 52.5% and 28% of isolates from Six Runs Creek were associated with lagoon effluent and cattle manure, respectively.  The predominant sources of fecal pollution identified in this study were equivalent to a previous traditional antibiotic resistance analysis (ARA) study that used an ARA library with an ARCC of 94.3% and implicated an association of 64% of isolates with lagoon liquid and 27.1% cattle manure. The results of the current study indicate that ARG profiles may have potential as a microbial source tracking tool.  However, developing a library with a high ARCC composed of individual host source categories may be difficult due to the high variability of ARGs within individual hosts.