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Team Detects Antibiotic Resistance Genes in Chinese Pig Farm Samples

NEW YORK (GenomeWeb News) – American and Chinese researchers have used quantitative PCR arrays to begin documenting the presence of diverse antibiotic resistance genes in manure and soil samples from commercial swine farms in China.

The Michigan State University and Chinese Academy of Sciences-led team tested manure, compost, and soil samples from three large Chinese swine farms where antibiotics and heavy metals such as zinc, copper, and arsenic are used for animal food supplementation and therapeutics. The analysis, published online this week in the Proceedings of the National Academy of Sciences, revealed nearly 150 distinct antibiotic resistance genes in the swine farm samples.

A subset of the resistance genes was present at especially high levels in the agricultural samples compared to manure or soil from sites where antibiotics are less common, the researchers reported, and so, too, were sequences from some transposase enzymes suspected of contributing to resistance gene transfer from one host to another.

"Diverse, abundant, and potentially mobile [antibiotic resistance genes] in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of [antibiotic resistance genes] to the environment," the researchers wrote.

Though the study centered on sites in China — a major antibiotic producer and consumer — its authors argued that similar patterns are apt to appear in other places where antibiotics routinely enter the environment via animal waste.

"Multi-drug resistance is a global problem and must be addressed in a comprehensive manner," the Chinese Academy of Sciences' Yong-Guan Zhu, the study's first author, said in a statement. "[O]ne area that needs to be addressed is more judicious use and management of wastes that contain" antibiotic resistance genes.

For their study, Zhu and his colleagues focused on three dozen samples from large commercial swine farms in Beijing, Zhejian, and Fujian that housed 10,000 or more animals apiece, relying on high-capacity quantitative PCR arrays to test manure, manure compost, and manure compost-treated soil samples from each of the farms.

The Applied Biosystems OpenArray system used for this analysis was comprised of 313 primer pairs, which were used to test for the presence of 244 antibiotic resistance genes.

In addition to finding antibiotics and heavy metals in the soil and manure samples tested, the researchers uncovered 149 distinct antibiotic resistance genes at the swine farms — three times the resistance gene diversity they detected in control samples from antibiotic and heavy metal-free sites.

These manure and soil-associated sequences represented a wide range of known resistance genes, the team noted, including genes associated with the ability to grow in the presence of antibiotics not used at a given farm.

Not only the diversity but also the levels of resistance genes were enhanced at the commercial swine sites tested, the researchers found, with the top 63 resistance genes turning up at levels anywhere from 192 times to 28,000 times above those observed in control samples.

The control samples — which included soil samples from an uncontaminated forest site in China and manure samples from pigs that had never received antibiotics in their feed — also contained far fewer sequences representing transposase enzymes suspected of spurring horizontal gene transfer of some resistance genes.

"The co-enrichment of [antibiotic resistance genes] and transposases further exacerbates the risk of transfer of [antibiotic resistance genes] from livestock animals to human-associated bacteria, and then spread among human populations," study authors wrote.

In general, the levels of antibiotics, heavy metals, and resistance genes tended to dip in the manure compost-treated soil samples relative to the original manure samples tested. And the presence of persistent resistance genes in soil might depend somewhat on the extent to which manure gets composted, the researchers added.

Still, they said, in the current study, some soil samples contained resistance genes at levels that were roughly 1,000-fold beyond those detected in the control soil, suggesting antibiotic resistance-related environmental contamination may occur via not only manure itself, but also resistance gene-exposed soil.

"Microbes from manure, compost, or soil containing the [antibiotic resistance genes] are subject to dispersal via runoff into rivers, leaching to sub-surface waters, air dispersal via dust, human travel, and distribution of agricultural products," the team noted, "including compost for gardening, which could expand a local contamination to regional and even global scales."