Aerobic Composting and Anaerobic Digestion Decrease the Copy Numbers of Antibiotic-Resistant Genes and the Levels of Lactose-Degrading Enterobacteriaceae in Dairy Farms in Hokkaido, Japan

Satoshi Katada; Akira Fukuda; Chie Nakajima; Yasuhiko Suzuki; Takashi Azuma; Ayaka Takei; Hideshige Takada; Eiryu Okamoto; Toshihide Kato; Yutaka Tamura; Masaru Usui

doi:10.3389/fmicb.2021.737420

Aerobic Composting and Anaerobic Digestion Decrease the Copy Numbers of Antibiotic-Resistant Genes and the Levels of Lactose-Degrading Enterobacteriaceae in Dairy Farms in Hokkaido, Japan

Front Microbiol. 2021 Sep 30:12:737420. doi: 10.3389/fmicb.2021.737420. eCollection 2021.

Authors

Satoshi Katada¹, Akira Fukuda¹, Chie Nakajima^{2

3}, Yasuhiko Suzuki^{2

3}, Takashi Azuma⁴, Ayaka Takei⁵, Hideshige Takada⁵, Eiryu Okamoto⁶, Toshihide Kato⁷, Yutaka Tamura¹, Masaru Usui¹

Affiliations

¹ Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan.
² Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.
³ International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
⁴ Department of Pharmacy, Osaka Medical and Pharmaceutical University, Takatsuki, Japan.
⁵ Laboratory of Organic Geochemistry, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan.
⁶ Laboratory of Environmental Microbiology, College of Agriculture, Food, and Environment Sciences, Rakuno Gakuen University, Ebetsu, Japan.
⁷ Department of Large Animal Clinical Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan.

Abstract

Efficient methods for decreasing the spread of antimicrobial resistance genes (ARGs) and transfer of antimicrobial-resistant bacteria (ARB) from livestock manure to humans are urgently needed. Aerobic composting (AC) or anaerobic digestion (AD) are widely used for manure treatment in Japanese dairy farms. To clarify the effects of AC and AD on antimicrobial resistance, the abundances of antimicrobial (tetracycline and cefazolin)-resistant lactose-degrading Enterobacteriaceae as indicator bacteria, copy numbers of ARGs (tetracycline resistance genes and β-lactamase coding genes), and concentrations of residual antimicrobials in dairy cow manure were determined before and after treatment. The concentration of tetracycline/cefazolin-resistant lactose-degrading Enterobacteriaceae was decreased over 1,000-fold by both AC and AD. ARGs such as tetA, tetB, and bla _TEM were frequently detected and their copy numbers were significantly reduced by ∼1,000-fold by AD but not by AC. However, several ARG copies remained even after AD treatment. Although concentrations of the majority of residual antimicrobials were decreased by both AC and AD, oxytetracycline level was not decreased after treatment in most cases. In addition, 16S rRNA gene amplicon-based metagenomic analysis revealed that both treatments changed the bacterial community structure. These results suggest that both AC and AD could suppress the transmission of ARB, and AD could reduce ARG copy numbers in dairy cow manure.

Keywords: aerobic composting; ampicillin resistance; anaerobic digestion; antimicrobial resistance; dairy cow; tetracycline resistance.