Tetracycline Resistome of the Organic Pig Gut

Abstract

The occurrence of genes conferring resistance to tetracyclines in the organic pig gut was assessed through the metagenomic approach. Of 9,000 bacterial artificial chromosome clones analyzed, 10 were identified as carrying the known tet(C), tet(W), and tet(40) genes, as well as novel genes encoding resistance to the tetracyclines minocycline and doxycycline. The latter are different from the known tet genes and are homologous to genes encoding UDP-glucose 4-epimerases, with the domain structure characteristic for these enzymes. The majority of the resistance genes were associated with putative mobile genetic elements. The sequence of a novel 9.7-kb plasmid carrying tet(W) and tet(40) was also identified. Conserved flanking regions identified around the tet(W) and tet(40) genes in our metagenomic library may play a role in genetic exchange of these genes. This is the first report describing the occurrence of tet(40) outside the human intestine. The maintenance of antibiotic resistance genes in apparently antibiotic-free animals is probably due to their presence on mobile genetic elements, the fitness cost of which for the cell is ameliorated during the previous antibiotic selection.

Chlortetracycline-Resistant Intestinal Bacteria in Organically Raised and Feral Swine

“…Eight organic and three feral swine isolates did not have detectable tet genes ( Table 4), suggesting that their resistance genes have minor sequence differences in regions targeted by the PCR primers (13) or represent a tet class not targeted in this study (5,10,21). Most CTC-resistant swine isolates (99/ 110) were positive in PCR assays for tet genes (Table 4).…”

Influence of Soil Use on Prevalence of Tetracycline, Streptomycin, and Erythromycin Resistance and Associated Resistance Genes

“…6B) soils, suggest that resistance to the tested antibiotics may be associated with transposons (20). It is unclear whether this indicates selection of resistant resident members of the soil community, proliferation of bacteria introduced via manure amendments, and/or dissemination of mobile genetic elements and horizontal gene transfer (5,6,12,16,17,28).…”

Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China

“…However, activity-based functional screening of metagenomic libraries, which provide direct evidence for antibiotic resistant phenotype, still remains a critical means to discover novel ARGs and identify their function that could be missed when using sequence based analysis only. Using functional screening of metagenomic libraries, novel functional ARGs have been identified from human microbiome (Sommer et al, 2009), organic pig gut (Kazimierczak et al, 2009), activated sludge (Mori et al, 2008) and soils (Allen et al, 2009;Lang et al, 2010;McGarvey et al, 2012). Most of these ARGs have not been identified previously and are evolutionarily distant from known resistance genes.…”