Diverse and abundant antibiotic resistance genes in Chinese swine farms

Abstract

Antibiotic resistance genes (ARGs) are emerging contaminants posing a potential worldwide human health risk. Intensive animal husbandry is believed to be a major contributor to the increased environmental burden of ARGs. Despite the volume of antibiotics used in China, little information is available regarding the corresponding ARGs associated with animal farms. We assessed type and concentrations of ARGs at three stages of manure processing to land disposal at three large-scale (10,000 animals per year) commercial swine farms in China. In-feed or therapeutic antibiotics used on these farms include all major classes of antibiotics except vancomycins. High-capacity quantitative PCR arrays detected 149 unique resistance genes among all of the farm samples, the top 63 ARGs being enriched 192-fold (median) up to 28,000-fold (maximum) compared with their respective antibiotic-free manure or soil controls. Antibiotics and heavy metals used as feed supplements were elevated in the manures, suggesting the potential for coselection of resistance traits. The potential for horizontal transfer of ARGs because of transposon-specific ARGs is implicated by the enrichment of transposases—the top six alleles being enriched 189-fold (median) up to 90,000-fold in manure—as well as the high correlation ( r 2 = 0.96) between ARG and transposase abundance. In addition, abundance of ARGs correlated directly with antibiotic and metal concentrations, indicating their importance in selection of resistance genes. Diverse, abundant, and potentially mobile ARGs in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of ARGs to the environment.

Antibiotic resistance genes in manure-amended soil and vegetables at harvest

“…Horizontal gene transfer could potentially enhance the accumulation and persistence of ARGs in manure-amended soil via MGEs [8]. In this study, it was found that intI1 gene had significantly positive correlation with sulI, sulII, tetA, tetC, tetG, and tetBP genes, indicating that intI1 gene may play certain role in the dissemination of ARGs.…”

“…As stated above, not only antibiotics but also considerable numbers of antibioticresistant bacteria, ARGs and associated MGEs are introduced to soil via manure application [8]. Tet genes have been commonly detected in soil adjacent to representative swine feedlots in China [34].…”

Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters

“…The total length of the river with tributaries is 1178 km, and the length of the main stem is 33.9 km (Mei et al 2014). High-throughput quantitative PCR (HT-qPCR) with 296 primer sets (285 ARGs, 9 transposase genes, one class 1 integron-integrase gene, and the bacterial 16S ribosomal RNA (rRNA) gene) was used to detect microbial community composition and ARG profiles (Zhu et al 2013).…”

“…A total of 296 primer sets targeted 285 ARGs, 9 transposases, one clinical class 1 integron-integrase gene, and 16S rRNA genes (Zhu et al 2013;Su et al 2015). The 285 ARGs conferred resistance to almost all major antibiotics (aminoglycoside, beta-lactams, fluoroquinolone/quinolone/florfenicol/chloramphenicol/amphenicol (FCA), macrolide/lincosamide/ streptogramin B (MLSB), sulfonamide, tetracycline, vancomycin, and genes coding multidrug efflux pumps or antibiotic deactivation protein resistance to other antibiotic and bactericide (other/efflux)) and covered three resistance mechanisms (antibiotic deactivation, efflux pumps, and cellular protection).…”

Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil

“…Land application of sewage sludge may result in the spread of ARGs in soil and to underground water (Threedeach et al, 2012). More importantly, bacteria have been shown to readily share genetic information by HGT via mobile genetic elements (MGEs) including plasmids, transposons, and integrons (Zhu et al, 2013;Pruden et al, 2006), allowing the transfer of resistance genes from sewage sludge microorganisms to indigenous environmental bacteria (Gaze et al, 2011). Sewage sludge has been shown to be a hotspot for bacteria carrying ARGs and MGEs and its application may enhance the HGT of ARGs in soil, although the bacterial populations of sewage sludge and soil may be quite distinct (Hammesfahr et al, 2008).…”