Duck wastes as a potential reservoir of novel antibiotic resistance genes

• Published in: The Science of the total environment Vol. 771; p. 144828
• Main Authors: Wang, Xi-Ran, Lian, Xin-Lei, Su, Tian-Tian, Long, Teng-Fei, Li, Meng-Yuan, Feng, Xiao-Yin, Sun, Ruan-Yang, Cui, Ze-Hua, Tang, Tian, Xia, Jing, Huang, Ting, Liu, Ya-Hong, Liao, Xiao-Ping, Fang, Liang-Xing, Sun, Jian
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2021
• Subjects: Animal wastes; Animals; Anti-Bacterial Agents - pharmacology; Antibiotic resistance genes; beta-Lactamases - genetics; China; Drug Resistance, Microbial - genetics; Duck; Ducks; Functional metagenomics; Genes, Bacterial; Novel genes; Reservoir; China; Duck; Reservoir; Functional metagenomics; Animal wastes; Novel genes; Antibiotic resistance genes
• ISSN: 0048-9697; 1879-1026
• DOI: 10.1016/j.scitotenv.2020.144828

Overuse of antibiotics in animal husbandry has led to an increase of antibiotic resistance microorganisms as well as antibiotic-resistance genes (ARGs). Duck farming in China is practiced on a large and diverse scale and the overuse of antibiotics in this field is gaining attention recently. We evaluated the diversity of ARGs from five duck farms using a functional metagenomic approach and constructed five libraries. A total of seventy-six resistant determinants were identified, of which sixty-one were gene variants or novel genes. The novel genes contained five β-lactamase-encoding genes designated as blaDWA1, blaDWA2, blaDWA3, blaDWA4 and blaDWB1, respectively, and two genes conferring resistance to fosfomycin designated as fosA-like1 and fosA-like2. Three of the five β-lactamase-encoding genes were further identified as extended-spectrum β-lactamases (ESBL) that can hydrolyze both penicillins and cephalosporins. Besides, two of the five β-lactamase-encoding genes were associated with mobile genetic elements, indicating a high potential for transfer of the genes to other bacterial hosts. The two novel fosA-like genes were able to increase the MICs of the test Escherichia coli strain from 2 μg/mL to as high as 256 μg/mL(up to 128-fold increase). Our study provides a reference for ARGs prevalence in duck farm wastes and implies that they are an important resistome reservoir, especially for novel ARGs with high spread potential. [Display omitted] •Duck wastes were a potential reservoir of novel antibiotic resistance genes.•The novel antibiotic resistance detected indicated a high potential for transmission.•The Proteobacteria was the most common host phyla detected through functional selections.•Functional metagenomics was a powerful and alternative strategy to study the resistome.