AUTHOR=Neher Timothy P. , Soupir Michelle L. , Andersen Daniel S. , O’Neill Maggie L. , Howe Adina 

TITLE=Comparison of antibiotic resistance genes in swine manure storage pits of Iowa, USA

JOURNAL=Frontiers in Antibiotics

VOLUME=2

YEAR=2023

URL=https://www.frontiersin.org/journals/antibiotics/articles/10.3389/frabi.2023.1116785

DOI=10.3389/frabi.2023.1116785

ISSN=2813-2467

ABSTRACT=<p>Antimicrobial resistance (AMR) can develop in deep-pit swine manure storage when bacteria are selectively pressured by unmetabolized antibiotics. Subsequent manure application on row crops is then a source of AMR into soil and downstream runoff water. Therefore, understanding the patterns of diverse antibiotic resistance genes (ARGs) in manure among different farms is important for both interpreting the results of the detection of these genes from previous studies and for the use of these genes as bioindicators of manure borne antibiotic resistance in the environment. Previous studies of manure-associated ARGs are based on limited samples of manures. To better understand the distribution of ARGs between manures, we characterized manures from 48 geographically independent swine farms across Iowa. The objectives of this study were to characterize the distribution of ARGs among these manures and to evaluate what factors in manure management may influence the presence of ARGs in manures. Our analysis included quantification of two commonly found ARGs in swine manure, <italic>ermB</italic> and <italic>tetM</italic>. Additionally, we characterized a broader suite of 31 ARGs which allowed for simultaneous assays of the presence or absence of multiple genes. We found the company integrator had a significant effect on both <italic>ermB</italic> (<italic>P=0.0007</italic>) and <italic>tetM</italic> gene concentrations (<italic>P=0.0425</italic>). Our broad analysis on ARG profiles found that the <italic>tet(36)</italic> gene was broadly present in swine manures, followed by the detection of <italic>tetT</italic>, <italic>tetM</italic>, <italic>erm(35)</italic>, <italic>ermF</italic>, <italic>ermB</italic>, <italic>str</italic>, <italic>aadD</italic>, and <italic>intl3</italic> in samples from 14 farms. Finally, we provide a comparison of methods to detect ARGs in manures, specifically comparing conventional and high-throughput qPCR and discuss their role in ARG environmental monitoring efforts. Results of this study provide insight into commonalities of ARG presence in manure holding pits and provide supporting evidence that company integrator decisions may impact ARG concentrations.</p>