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Environ Pollut. 2019 Nov;254(Pt B):113058. doi: 10.1016/j.envpol.2019.113058. Epub 2019 Aug 14.

Dairy farm soil presents distinct microbiota and varied prevalence of antibiotic resistance across housing areas.

Author information

1
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China; Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, Jiangsu, PR China; Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, CA 95616, USA.
2
Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, Jiangsu, PR China.
3
Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA.
4
Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA; Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA, USA.
5
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China. Electronic address: zhanganyun@scu.edu.cn.

Abstract

Dairy cattle of different ages experience different living conditions and varied frequency of antibiotic administration that likely influence the distribution of microbiome and resistome in ways that reflect different risks of microbial transmission. To assess the degree of variance in these distributions, fecal and soil samples were collected from six distinct housing areas on commercial dairy farms (n = 7) in Washington State. 16S rRNA gene sequencing indicated that the microbiota differed between different on-farm locations in feces and soil, and in both cases, the microbiota of dairy calves was often distinct from others (P < 0.05). Thirty-two specific antibiotic resistance genes (ARGs) were widely distributed on dairies, of which several clinically relevant ARGs (including cfr, cfrB, and optrA) were identified for the first time at U.S. dairies. Overall, ARGs were observed more frequently in feces and soil from dairy calves and heifers than from hospital, fresh, lactation and dry pens. Droplet-digital PCR demonstrated that the absolute abundance of floR varied greatly across housing areas and this gene was enriched the most in calves and heifers. Furthermore, in an extended analysis with 14 dairies, environmental soils in calf pens had the most antibiotic-resistant Escherichia coli followed by heifer and hospital pens. All soil E. coli isolates (n = 1,905) are resistant to at least 4 different antibiotics, and the PFGE analysis indicated that florfenicol-resistant E. coli is probably shared across geographically-separated farms. This study identified a discrete but predictable distribution of antibiotic resistance genes and organisms, which is important for designing mitigation for higher risk areas on dairy farms.

KEYWORDS:

Antibiotic resistance; Calf; Dairy farm; Discrete distribution; Housing areas; Soil

PMID:
31454571
DOI:
10.1016/j.envpol.2019.113058
[Indexed for MEDLINE]

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