Antibiotic Resistance Genes in Cattle Gut Mictobiota: Influence of Housing Conditions

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Abstract

Resistance to antimicrobial drugs is an urgent problem not only in public health, but also in animal husbandry. The widespread use of antimicrobials in feed additives is one of the main reasons for the rapid spread of antibiotic resistance in the microbiota of the gastrointestinal tract of farm animals. To characterize antibiotic resistance genes (resistome), we performed metagenomic analysis of feces of 24 cattle from different regions of Russia, including cows of different breeds and yaks. Animals differed in the type of housing: year-round on pastures or in barns of conventional farms, with consumption of feed additives. Although genes of resistance to aminoglycosides, β-lactams, glycopeptides, MLS antibiotics (macrolides, lincosamides and streptogramins), phenicols and tetracyclines were detected in samples from both groups of animals, the content of resistome in the fecal microbiome of stall-bred cattle was about 10 times higher than in animals kept on pastures. The resistome of stall cattle was dominated by β-lactamases and tetracycline resistance genes, whose content in the microbiome was 24 and 60 times higher, respectively, than in animals kept on pastures. Apparently, the spread of resistance to β-lactams and tetracyclines in stall cattle reflects the active use of these antibiotics in livestock production. Metagenomic analysis of livestock feces can be used to quantify antibiotic resistance genes for the purpose of monitoring antimicrobial drugs used in animal husbandry.

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About the authors

Sh. A. Begmatov

Research Center of Biotechnology of the Russian Academy of Sciences

Author for correspondence.
Email: shabegmatov@gmail.com
Russian Federation, Moscow, 119071

A. V. Beletsky

Research Center of Biotechnology of the Russian Academy of Sciences

Email: shabegmatov@gmail.com
Russian Federation, Moscow, 119071

A. L. Rakitin

Research Center of Biotechnology of the Russian Academy of Sciences

Email: shabegmatov@gmail.com
Russian Federation, Moscow, 119071

A. P. Lukina

Tomsk State University

Email: shabegmatov@gmail.com
Russian Federation, Tomsk, 634050

L. O. Sokolyanskaya

Tomsk State University

Email: shabegmatov@gmail.com
Russian Federation, Tomsk, 634050

A. V. Rakitin

Tomsk State University

Email: shabegmatov@gmail.com
Russian Federation, Tomsk, 634050

L. B. Glukhova

Tomsk State University

Email: shabegmatov@gmail.com
Russian Federation, Tomsk, 634050

A. V. Mardanov

Research Center of Biotechnology of the Russian Academy of Sciences

Email: shabegmatov@gmail.com
Russian Federation, Moscow, 119071

O. V. Karnachuk

Tomsk State University

Email: shabegmatov@gmail.com
Russian Federation, Tomsk, 634050

N. V. Ravin

Research Center of Biotechnology of the Russian Academy of Sciences

Email: shabegmatov@gmail.com
Russian Federation, Moscow, 119071

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Supplementary files

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3. Fig. 1. Taxonomic composition of microbial communities of fecal samples of Galloway cattle (1), yaks (2) and “stable” cattle (3). The figure shows phylum, the average proportion of which in the communities is at least 1%.

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4. Fig. 2. Fecal sample resistomes classified by ARG family. The ordinate axis indicates the number of ARGS identified in the metagenome, by 109 nucleotides of the total length of the collected contigues. The following gene clusters are shown on the right (from top to bottom): streptogramin-acetyltransferase; class A beta-lactamase; tetracycline-resistant ribosome protection protein; metallo-beta-lactamase; lincosamide-nucleotidyltransferase; chloramphenicol-acetyltransferase; glycopeptide resistance gene cluster; ABC-F type ribosome protection proteins; aminoglycoside phosphotransferase.

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5. Fig. 3. The relative content of ARG in the intestinal microbiome of Galloway cattle, yaks and “stable” cattle is presented by classes of antibiotics. The ordinate axis indicates the ARG content in the fecal metagenome, normalized to the content of 16S rRNA genes. The left part of the figure shows data for Galloway cattle and yaks on an enlarged scale. The following classes of antibiotics are shown on the right (from top to bottom): tetracyclines, phenicols, MLS group, glycopeptides, beta-lactams, aminoglycosides.

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