Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Authors: Ibekwe, Abasiofiok - Mark; BHATTACHARJEE, ANANDA - University Of California, Riverside; PHAN, DUC - University Of California, Riverside; Ashworth, Daniel; Schmidt, Michael - Mike; MURINDA, SHELTON - California Polytechnic State University; OBAYIUWANA, AMARACHUKWU - Augustine University Ilara; MURRY, MARCIA - California Polytechnic State University; SCHWARTZ, GREGORY - California Polytechnic State University; LUNDQUIST, TRYGV - California Polytechnic State University; MA, JINCAI - Jilin University; KARATHIA, H. - Cosmosid; FANELLI, B. - Cosmosid; HASAN, N. - University Of Maryland; YANG, CHING-HONG - University Of Wisconsin

Submitted to: Science of the Total Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2023
Publication Date: 2/11/2023
Citation: Ibekwe, A.M., Bhattacharjee, A.S., Phan, D., Ashworth, D.J., Schmidt, M.P., Murinda, S.E., Obayiuwana, A., Murry, M.A., Schwartz, G., Lundquist, T., Ma, J., Karathia, H., Fanelli, B., Hasan, N.A., Yang, C. 2023. Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land. Science of the Total Environment. 872. Article 162194. https://doi.org/10.1016/j.scitotenv.2023.162194.
DOI: https://doi.org/10.1016/j.scitotenv.2023.162194

Interpretive Summary: Antibiotic-resistant bacteria can be transferred from animals to humans by direct contact, and can spread to soil, food, and groundwater through the application of manure to agricultural fields. The objective of this research was to understand the dissemination routes of antibiotic resistance genes, antibiotic-resistant bacteria, and virulence factor genes from manure and wastewater to agricultural fields. Our study showed that aminoglycosides, tetracyclines, beta lactam, and macrolides were the main antibiotics resistance gene classes found in our samples. This study demonstrates that dissemination of waste from these sources can increase the spread of these chemicals into agricultural lands with a negative impact on both soil and human health. The results of this research will be used by growers, researchers, FSIS, FDA, and different state agencies.

Technical Abstract: Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a wastewater treatment plant along the waste coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARGs were observed between pig manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55%), tetracyclines (30–45%), beta-lactam-resistance (20-35%), macrolides (18-30%), and more than 50 % of the VFGs that the 24 microbiomes harbor were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. KEGG metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with Carbapenem resistance, MDR, and efflux pump, and Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands with a negative impact on both soil and human health.