Quantification of antibiotic resistance genes and mobile genetic in dairy manure

Yi Wang; Pramod Pandey; Colleen Chiu; Richard Jeannotte; Sundaram Kuppu; Ruihong Zhang; Richard Pereira; Bart C Weimer; Nitin Nitin; Sharif S Aly

doi:10.7717/peerj.12408

Quantification of antibiotic resistance genes and mobile genetic in dairy manure

PeerJ. 2021 Dec 23:9:e12408. doi: 10.7717/peerj.12408. eCollection 2021.

Authors

Yi Wang¹, Pramod Pandey¹, Colleen Chiu¹, Richard Jeannotte^{1

2}, Sundaram Kuppu¹, Ruihong Zhang³, Richard Pereira¹, Bart C Weimer¹, Nitin Nitin⁴, Sharif S Aly^{1

5}

Affiliations

¹ Department of Population Health and Reproduction, University of California, Davis, Davis, California, United States.
² Department of Plant Science, University of California, Davis, Davis, California, United States.
³ Department of Biological and Agricultural Engineering, University of California, Davis, Davis, California, United States.
⁴ Department of Food Science and Technology, University of California, Davis, Davis, California, United States.
⁵ Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Davis, California, United States.

Abstract

Background: Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure.

Methods: This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLS_B) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1).

Results: Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

Keywords: Antibiotic resistance genes; Dairy manure; Gene sequencing; Mobile genetic elements; Real-time pcr.

Grants and funding

This work was supported by the USDA National Institute of Food and Agriculture through Center for Food Animal Health (CFAH), Animal Health Project (Accession Number CALV-AH-367), University of California-Davis, Davis, California. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.